chr7-117610523-TATTA-T

Position:

• chr7-117610523-TATTA-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000492.4(CFTR):​c.2997_3000del​(p.Ile1000Ter) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,904 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. L998L) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: CFTR NM_000492.4 frameshift
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:6
• Conservation: PhyloP100: 7.62

Genes affected

CFTR (HGNC:1884): (CF transmembrane conductance regulator) This gene encodes a member of the ATP-binding cassette (ABC) transporter superfamily. The encoded protein functions as a chloride channel, making it unique among members of this protein family, and controls ion and water secretion and absorption in epithelial tissues. Channel activation is mediated by cycles of regulatory domain phosphorylation, ATP-binding by the nucleotide-binding domains, and ATP hydrolysis. Mutations in this gene cause cystic fibrosis, the most common lethal genetic disorder in populations of Northern European descent. The most frequently occurring mutation in cystic fibrosis, DeltaF508, results in impaired folding and trafficking of the encoded protein. Multiple pseudogenes have been identified in the human genome. [provided by RefSeq, Aug 2017]

(HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 7-117610523-TATTA-T is Pathogenic according to our data. Variant chr7-117610523-TATTA-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 53618.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFTR	NM_000492.4	c.2997_3000del	p.Ile1000Ter	frameshift_variant	19/27	ENST00000003084.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFTR	ENST00000003084.11	c.2997_3000del	p.Ile1000Ter	frameshift_variant	19/27	1	NM_000492.4	P2
	ENST00000456270.1	n.178-5538_178-5535del		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.85e-7 AC: 1 AN: 1460904 Hom.: 0 AF XY: 0.00000138 AC XY: 1 AN XY: 726784

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Cystic fibrosis Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	Nov 05, 2018	- -
Pathogenic, criteria provided, single submitter	curation	CFTR-France	Jan 29, 2018	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Counsyl	May 11, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Aug 01, 2022	The c.2997_3000delAATT pathogenic mutaiton, located in coding exon 19 of the CFTR gene, results from a deletion of 4 nucleotides at nucleotide positions 2997 to 3000, causing a translational frameshift with a predicted alternate stop codon (p.I1000*). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This alteration has been detected in the homozygous state, or in conjunction with another CFTR pathogenic mutation, in multiple unrelated individuals with cystic fibrosis or CFTR-related disorders (AbdulWahab A et al. Qatar Med J, 2021 Jul;2021:24; Liu K et al. Orphanet J Rare Dis, 2020 06;15:150; El-Seedy A et al. Cell Mol Biol (Noisy-le-grand), 2016 Nov;62:21-28). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Sep 18, 2021	For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 53618). This variant is also known as 3126del4 and/or 3129del4. This premature translational stop signal has been observed in individual(s) with CFTR-related conditions (PMID: 11788090, 32539862). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Ile1000*) in the CFTR gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CFTR are known to be pathogenic (PMID: 1695717, 7691345, 9725922). -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 16, 2024	Variant summary: CFTR c.2997_3000delAATT (p.Ile1000X) results in a premature termination codon, predicted to cause absence of the protein due to nonsense mediated decay, which is a commonly known mechanism for disease. The variant was absent in 251116 control chromosomes (gnomAD). c.2997_3000delAATT has been reported in the literature in individuals affected with Cystic Fibrosis (e.g. Liu_2020, AbdulWahab_2021). The following publications have been ascertained in the context of this evaluation (PMID: 32539862, 34377682). ClinVar contains an entry for this variant (Variation ID: 53618). Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs397508472; hg19: chr7-117250577;