chr4-112646005-G-GTT

Position:

• chr4-112646005-G-GTT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_016648.4(LARP7):​c.203-344_203-343dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 150,724 control chromosomes in the GnomAD database, including 7,614 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.27 (7614 hom., cov: 23)
• Consequence: LARP7 NM_016648.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.297

Genes affected

LARP7 (HGNC:24912): (La ribonucleoprotein 7, transcriptional regulator) This gene encodes a protein which is found in the 7SK snRNP (small nuclear ribonucleoprotein). This snRNP complex inhibits a cyclin-dependent kinase, positive transcription elongation factor b, which is required for paused RNA polymerase II at a promoter to begin transcription elongation. A pseudogene of this gene is located on chromosome 3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 4-112646005-G-GTT is Benign according to our data. Variant chr4-112646005-G-GTT is described in ClinVar as [Benign]. Clinvar id is 1265867.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LARP7	NM_016648.4	c.203-344_203-343dup		intron_variant		ENST00000344442.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LARP7	ENST00000344442.10	c.203-344_203-343dup		intron_variant		2	NM_016648.4	P4

Frequencies

GnomAD3 genomes AF: 0.272 AC: 40949 AN: 150608 Hom.: 7583 Cov.: 23

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.272 AC: 41040 AN: 150724 Hom.: 7614 Cov.: 23 AF XY: 0.273 AC XY: 20089 AN XY: 73568

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.265

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5861107; hg19: chr4-113567161;