rs10036519

Variant names:

• chr5-140772116-A-G
• rs10036519

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 0.47 in 151,974 control chromosomes in the GnomAD database, including 17,455 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 0.47 (17455 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 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: 0.470 AC: 71410 AN: 151854 Hom.: 17453 Cov.: 33

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.470 AC: 71423 AN: 151974 Hom.: 17455 Cov.: 33 AF XY: 0.468 AC XY: 34782 AN XY: 74262

African (AFR) AF: 0.342 AC: 14181 AN: 41476

American (AMR) AF: 0.511 AC: 7799 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1802 AN: 3470

East Asian (EAS) AF: 0.518 AC: 2682 AN: 5176

South Asian (SAS) AF: 0.530 AC: 2557 AN: 4826

European-Finnish (FIN) AF: 0.440 AC: 4631 AN: 10528

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35853 AN: 67912

Other (OTH) AF: 0.484 AC: 1021 AN: 2110

Alfa AF: 0.496 Hom.: 6149

Bravo AF: 0.474

Asia WGS AF: 0.443 AC: 1539 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.7
DANN	Benign	0.39
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs10036519; hg19: chr5-140151701; COSMIC: COSV60202303;