rs10514713

Variant names:

• chr3-46502127-C-A
• rs10514713

Your query was ambiguous. Multiple possible variants found:

• chr3-46502127-C-A
• chr3-46502127-C-G

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 0.318 in 152,084 control chromosomes in the GnomAD database, including 9,292 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 0.32 (9292 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 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: 0.318 AC: 48291 AN: 151966 Hom.: 9285 Cov.: 32

Gnomad AFR AF: 0.0880

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.318 AC: 48298 AN: 152084 Hom.: 9292 Cov.: 32 AF XY: 0.323 AC XY: 23974 AN XY: 74326

African (AFR) AF: 0.0879 AC: 3648 AN: 41522

American (AMR) AF: 0.376 AC: 5751 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1630 AN: 3470

East Asian (EAS) AF: 0.483 AC: 2493 AN: 5164

South Asian (SAS) AF: 0.446 AC: 2144 AN: 4812

European-Finnish (FIN) AF: 0.430 AC: 4530 AN: 10530

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26996 AN: 67988

Other (OTH) AF: 0.316 AC: 668 AN: 2112

Alfa AF: 0.374 Hom.: 19261

Bravo AF: 0.305

Asia WGS AF: 0.431 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.7
DANN	Benign	0.77
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs10514713; hg19: chr3-46543617;