rs9273373

chr6-32658824-A-Gchr6-32658824-A-T

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 0.568 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.583

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9273373; hg19: chr6-32626601;