rs3907327

Variant names:

• chr6-79397865-T-G
• rs3907327

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0845 in 152,268 control chromosomes in the GnomAD database, including 599 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 0.084 (599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.118 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

Frequencies

GnomAD3 genomes AF: 0.0845 AC: 12864 AN: 152150 Hom.: 599 Cov.: 32

Gnomad AFR AF: 0.0418

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0907

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0845 AC: 12861 AN: 152268 Hom.: 599 Cov.: 32 AF XY: 0.0827 AC XY: 6157 AN XY: 74446

African (AFR) AF: 0.0417 AC: 1734 AN: 41570

American (AMR) AF: 0.0905 AC: 1385 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3464

East Asian (EAS) AF: 0.101 AC: 522 AN: 5174

South Asian (SAS) AF: 0.127 AC: 610 AN: 4816

European-Finnish (FIN) AF: 0.0518 AC: 550 AN: 10618

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7218 AN: 68012

Other (OTH) AF: 0.107 AC: 226 AN: 2110

Alfa AF: 0.0979 Hom.: 215

Bravo AF: 0.0852

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs3907327; hg19: chr6-80107582;