rs9275313

Variant names:

• chr6-32697982-G-T
• rs9275313

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 0.1 in 139,408 control chromosomes in the GnomAD database, including 821 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 0.10 (821 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.188 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: 0.100 AC: 13960 AN: 139296 Hom.: 820 Cov.: 30

Gnomad AFR AF: 0.0406

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.0892

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.100 AC: 13980 AN: 139408 Hom.: 821 Cov.: 30 AF XY: 0.102 AC XY: 6973 AN XY: 68048

Gnomad4 AFR AF: 0.0408

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0881

Gnomad4 SAS AF: 0.0890

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.100

Alfa AF: 0.111 Hom.: 989

Bravo AF: 0.0987

Asia WGS AF: 0.0600 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275313; hg19: chr6-32665759;