6-67176026-A-G

Variant names:

• chr6-67176026-A-G
• rs9342616

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 0.574 in 151,052 control chromosomes in the GnomAD database, including 25,127 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 0.57 (25127 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.574 AC: 86701 AN: 150936 Hom.: 25100 Cov.: 31

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.574 AC: 86776 AN: 151052 Hom.: 25127 Cov.: 31 AF XY: 0.577 AC XY: 42561 AN XY: 73700

African (AFR) AF: 0.635 AC: 26157 AN: 41194

American (AMR) AF: 0.571 AC: 8648 AN: 15134

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2134 AN: 3446

East Asian (EAS) AF: 0.711 AC: 3631 AN: 5108

South Asian (SAS) AF: 0.673 AC: 3230 AN: 4802

European-Finnish (FIN) AF: 0.551 AC: 5748 AN: 10428

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35523 AN: 67632

Other (OTH) AF: 0.569 AC: 1198 AN: 2104

Alfa AF: 0.562 Hom.: 18381

Bravo AF: 0.577

Asia WGS AF: 0.699 AC: 2417 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.52
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs9342616; hg19: chr6-67885919;