rs7762319

Variant names:

• chr6-3854541-G-A
• rs7762319
• ENST00000454396.2:n.80-929G>A

Variant summary

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

The ENST00000454396.2(ENSG00000238158):​n.80-929G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,142 control chromosomes in the GnomAD database, including 12,343 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 0.39 (12343 hom., cov: 33)
• Consequence: ENSG00000238158 ENST00000454396.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

Genes affected

ENSG00000238158 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000238158	ENST00000454396.2	n.80-929G>A		intron_variant	Intron 1 of 1	5
ENSG00000233068	ENST00000648025.1	n.77-22498G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58717 AN: 152024 Hom.: 12341 Cov.: 33

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.386 AC: 58755 AN: 152142 Hom.: 12343 Cov.: 33 AF XY: 0.389 AC XY: 28928 AN XY: 74362

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.354

Alfa AF: 0.442 Hom.: 1974

Bravo AF: 0.359

Asia WGS AF: 0.222 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.9
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7762319; hg19: chr6-3854775;