chr6-32658824-A-G

Variant names:

• chr6-32658824-A-G
• rs9273373

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 0.568 in 151,310 control chromosomes in the GnomAD database, including 24,732 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 (24732 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.642 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: 0.569 AC: 85959 AN: 151194 Hom.: 24724 Cov.: 28

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.568 AC: 86014 AN: 151310 Hom.: 24732 Cov.: 28 AF XY: 0.565 AC XY: 41779 AN XY: 73888

African (AFR) AF: 0.516 AC: 21250 AN: 41174

American (AMR) AF: 0.653 AC: 9916 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2176 AN: 3464

East Asian (EAS) AF: 0.608 AC: 3120 AN: 5134

South Asian (SAS) AF: 0.508 AC: 2422 AN: 4764

European-Finnish (FIN) AF: 0.517 AC: 5408 AN: 10462

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.586 AC: 39751 AN: 67816

Other (OTH) AF: 0.583 AC: 1224 AN: 2100

Alfa AF: 0.585 Hom.: 2807

Bravo AF: 0.584

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.86
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs9273373; hg19: chr6-32626601;