rs9263846

Variant names:

• chr6-31187893-G-A
• rs9263846

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 0.164 in 151,976 control chromosomes in the GnomAD database, including 2,309 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 (2309 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 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: 0.164 AC: 24950 AN: 151858 Hom.: 2308 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.164 AC: 24970 AN: 151976 Hom.: 2309 Cov.: 31 AF XY: 0.170 AC XY: 12602 AN XY: 74268

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.228

Alfa AF: 0.178 Hom.: 1714

Bravo AF: 0.164

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.9
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: rs9263846; hg19: chr6-31155670;