rs10511321

Variant names:

• chr3-113194658-T-C
• rs10511321

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 0.039 in 152,272 control chromosomes in the GnomAD database, including 236 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 0.039 (236 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0878 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: 0.0389 AC: 5917 AN: 152154 Hom.: 232 Cov.: 33

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0912

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0389

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.00236

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00848

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0390 AC: 5937 AN: 152272 Hom.: 236 Cov.: 33 AF XY: 0.0388 AC XY: 2892 AN XY: 74452

African (AFR) AF: 0.0803 AC: 3335 AN: 41548

American (AMR) AF: 0.0918 AC: 1405 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3470

East Asian (EAS) AF: 0.0388 AC: 201 AN: 5184

South Asian (SAS) AF: 0.0207 AC: 100 AN: 4828

European-Finnish (FIN) AF: 0.00236 AC: 25 AN: 10614

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00848 AC: 577 AN: 68012

Other (OTH) AF: 0.0502 AC: 106 AN: 2112

Alfa AF: 0.0254 Hom.: 381

Bravo AF: 0.0499

Asia WGS AF: 0.0430 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.51
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs10511321; hg19: chr3-112913505;