6-32696222-G-C

Variant names:

• chr6-32696222-G-C
• rs6457620

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 0.519 in 151,732 control chromosomes in the GnomAD database, including 20,817 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 0.52 (20817 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979
• Publications: 92 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78641 AN: 151612 Hom.: 20792 Cov.: 31

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.519 AC: 78724 AN: 151732 Hom.: 20817 Cov.: 31 AF XY: 0.522 AC XY: 38654 AN XY: 74108

African (AFR) AF: 0.494 AC: 20448 AN: 41394

American (AMR) AF: 0.629 AC: 9603 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2118 AN: 3468

East Asian (EAS) AF: 0.565 AC: 2902 AN: 5138

South Asian (SAS) AF: 0.379 AC: 1830 AN: 4824

European-Finnish (FIN) AF: 0.582 AC: 6106 AN: 10492

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33757 AN: 67856

Other (OTH) AF: 0.543 AC: 1141 AN: 2100

Alfa AF: 0.517 Hom.: 2559

Bravo AF: 0.528

Asia WGS AF: 0.533 AC: 1858 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.40
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs6457620; hg19: chr6-32663999;