rs9275313

Positions:

• chr6-32697982-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 0.1 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;