rs10137732

Variant names:

• chr14-60222491-T-C
• rs10137732

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 0.372 in 152,052 control chromosomes in the GnomAD database, including 11,155 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 0.37 (11155 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56491 AN: 151930 Hom.: 11141 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.372 AC: 56544 AN: 152052 Hom.: 11155 Cov.: 32 AF XY: 0.367 AC XY: 27261 AN XY: 74312

African (AFR) AF: 0.508 AC: 21055 AN: 41464

American (AMR) AF: 0.286 AC: 4376 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1523 AN: 3468

East Asian (EAS) AF: 0.172 AC: 888 AN: 5174

South Asian (SAS) AF: 0.470 AC: 2262 AN: 4812

European-Finnish (FIN) AF: 0.294 AC: 3112 AN: 10568

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22305 AN: 67964

Other (OTH) AF: 0.352 AC: 744 AN: 2112

Alfa AF: 0.342 Hom.: 4048

Bravo AF: 0.375

Asia WGS AF: 0.304 AC: 1056 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.45
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10137732; hg19: chr14-60689209;