rs7762319

chr6-3854541-G-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, non coding transcript 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: ENST00000454396.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000454396.2	n.80-929G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000648025.1	n.77-22498G>A		intron_variant, non_coding_transcript_variant

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;