rs9275535

chr6-32708012-G-Achr6-32708012-G-Cchr6-32708012-G-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 0.589 in 151,764 control chromosomes in the GnomAD database, including 26,733 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 0.59 (26733 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 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: 0.590 AC: 89402 AN: 151646 Hom.: 26726 Cov.: 31

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.589 AC: 89457 AN: 151764 Hom.: 26733 Cov.: 31 AF XY: 0.590 AC XY: 43738 AN XY: 74160

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.640

Alfa AF: 0.574 Hom.: 3058

Bravo AF: 0.599

Asia WGS AF: 0.719 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	6.3
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275535; hg19: chr6-32675789;