rs9275772

Positions:

• chr6-32721726-T-C
• chr6-32721726-T-G

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 0.741 in 152,016 control chromosomes in the GnomAD database, including 42,256 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 0.74 (42256 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112629 AN: 151898 Hom.: 42222 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.741 AC: 112718 AN: 152016 Hom.: 42256 Cov.: 31 AF XY: 0.744 AC XY: 55334 AN XY: 74324

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.788

Alfa AF: 0.748 Hom.: 13798

Bravo AF: 0.734

Asia WGS AF: 0.870 AC: 3023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.5
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275772; hg19: chr6-32689503;