rs9268515

Positions:

• chr6-32411518-G-C
• chr6-32411518-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 0.16 in 113,414 control chromosomes in the GnomAD database, including 1,415 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 0.16 (1415 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.201 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: 0.160 AC: 18120 AN: 113322 Hom.: 1416 Cov.: 29

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.0751

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.160 AC: 18127 AN: 113414 Hom.: 1415 Cov.: 29 AF XY: 0.158 AC XY: 8697 AN XY: 55028

Gnomad4 AFR AF: 0.0511

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.0751

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0753 Hom.: 107

Bravo AF: 0.120

Asia WGS AF: 0.0710 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.29
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268515; hg19: chr6-32379295;