rs10514939

Variant names:

• chr5-62975261-C-T
• rs10514939

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 0.0463 in 152,206 control chromosomes in the GnomAD database, including 364 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 0.046 (364 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 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: 0.0461 AC: 7012 AN: 152088 Hom.: 359 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.00864

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0672

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00790

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0463 AC: 7047 AN: 152206 Hom.: 364 Cov.: 32 AF XY: 0.0454 AC XY: 3379 AN XY: 74416

African (AFR) AF: 0.123 AC: 5098 AN: 41502

American (AMR) AF: 0.0272 AC: 416 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00864 AC: 30 AN: 3472

East Asian (EAS) AF: 0.101 AC: 522 AN: 5182

South Asian (SAS) AF: 0.0676 AC: 326 AN: 4820

European-Finnish (FIN) AF: 0.00141 AC: 15 AN: 10608

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00791 AC: 538 AN: 68006

Other (OTH) AF: 0.0430 AC: 91 AN: 2114

Alfa AF: 0.0206 Hom.: 70

Bravo AF: 0.0505

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.59
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10514939; hg19: chr5-62271088;