rs9275495

Positions:

• chr6-32705797-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 0.0908 in 151,872 control chromosomes in the GnomAD database, including 810 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 0.091 (810 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32705797A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0907 AC: 13768 AN: 151756 Hom.: 809 Cov.: 32

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0751

Gnomad SAS AF: 0.0677

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0908 AC: 13787 AN: 151872 Hom.: 810 Cov.: 32 AF XY: 0.0926 AC XY: 6876 AN XY: 74270

Gnomad4 AFR AF: 0.0369

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.0753

Gnomad4 SAS AF: 0.0676

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0993

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.0929 Hom.: 78

Bravo AF: 0.0988

Asia WGS AF: 0.0600 AC: 210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.9
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275495; hg19: chr6-32673574;