rs3916765

chr6-32717773-G-A

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 0.0862 in 152,122 control chromosomes in the GnomAD database, including 705 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 0.086 (705 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 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: 0.0862 AC: 13105 AN: 152004 Hom.: 704 Cov.: 31

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0832

Gnomad SAS AF: 0.0616

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0741

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

GnomAD4 genome AF: 0.0862 AC: 13106 AN: 152122 Hom.: 705 Cov.: 31 AF XY: 0.0867 AC XY: 6445 AN XY: 74338

Gnomad4 AFR AF: 0.0221

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.0832

Gnomad4 SAS AF: 0.0616

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.106 Hom.: 740

Bravo AF: 0.0830

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	13
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3916765; hg19: chr6-32685550;