rs10832313

Variant names:

• chr11-14900817-A-G
• rs10832313

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.104 in 152,230 control chromosomes in the GnomAD database, including 1,080 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 (1080 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 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: 0.104 AC: 15746 AN: 152112 Hom.: 1077 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0656

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.0473

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0759

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.104 AC: 15775 AN: 152230 Hom.: 1080 Cov.: 33 AF XY: 0.101 AC XY: 7503 AN XY: 74438

African (AFR) AF: 0.192 AC: 7979 AN: 41512

American (AMR) AF: 0.0655 AC: 1002 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3470

East Asian (EAS) AF: 0.0460 AC: 239 AN: 5192

South Asian (SAS) AF: 0.0667 AC: 322 AN: 4828

European-Finnish (FIN) AF: 0.0473 AC: 501 AN: 10602

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0759 AC: 5164 AN: 68008

Other (OTH) AF: 0.103 AC: 217 AN: 2116

Alfa AF: 0.0900 Hom.: 442

Bravo AF: 0.110

Asia WGS AF: 0.0850 AC: 295 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.78
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10832313; hg19: chr11-14922363;