rs10512876

Variant names:

• chr5-45249502-T-C
• rs10512876

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 0.0493 in 152,274 control chromosomes in the GnomAD database, including 447 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 0.049 (447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.325 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: 0.0493 AC: 7495 AN: 152156 Hom.: 444 Cov.: 32

Gnomad AFR AF: 0.00878

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0357

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.0949

Gnomad FIN AF: 0.0919

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0493 AC: 7502 AN: 152274 Hom.: 447 Cov.: 32 AF XY: 0.0545 AC XY: 4057 AN XY: 74456

African (AFR) AF: 0.00876 AC: 364 AN: 41576

American (AMR) AF: 0.0361 AC: 553 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1752 AN: 5176

South Asian (SAS) AF: 0.0946 AC: 457 AN: 4832

European-Finnish (FIN) AF: 0.0919 AC: 973 AN: 10586

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0456 AC: 3100 AN: 68012

Other (OTH) AF: 0.0406 AC: 86 AN: 2116

Alfa AF: 0.0468 Hom.: 557

Bravo AF: 0.0442

Asia WGS AF: 0.176 AC: 612 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.62
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs10512876; hg19: chr5-45249604;