rs7760381

Positions:

• chr6-76680695-G-A
• chr6-76680695-G-T

Variant summary

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

The variant allele was found at a frequency of 0.195 in 151,728 control chromosomes in the GnomAD database, including 3,753 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 0.19 (3753 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 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

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29556 AN: 151610 Hom.: 3747 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0607

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.195 AC: 29585 AN: 151728 Hom.: 3753 Cov.: 32 AF XY: 0.195 AC XY: 14444 AN XY: 74174

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.0607

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.167

Alfa AF: 0.131 Hom.: 895

Bravo AF: 0.207

Asia WGS AF: 0.155 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7760381; hg19: chr6-77390412;