rs3907327

Positions:

• chr6-79397865-T-G

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 0.0845 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0417

Gnomad4 AMR AF: 0.0905

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0518

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0992 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3907327; hg19: chr6-80107582;