rs713134

Positions:

• chr7-117475202-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_927901.2(LOC105375468):​n.228-489C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,980 control chromosomes in the GnomAD database, including 27,986 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.57 (27986 hom., cov: 32)
• Consequence: LOC105375468 XR_927901.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

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]

LOC105375468 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375468	XR_927901.2	n.228-489C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFTR	ENST00000546407.1	n.49-489C>T		intron_variant, non_coding_transcript_variant		1
CFTR	ENST00000673785.1	c.-406+9371C>T		intron_variant				ENSP00000501235

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86616 AN: 151862 Hom.: 27920 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.521

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.571 AC: 86744 AN: 151980 Hom.: 27986 Cov.: 32 AF XY: 0.576 AC XY: 42753 AN XY: 74260

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.525

Alfa AF: 0.527 Hom.: 2931

Bravo AF: 0.578

Asia WGS AF: 0.583 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs713134; hg19: chr7-117115256;