rs10148587

Variant names:

• chr14-60222442-C-T
• rs10148587

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 0.394 in 151,926 control chromosomes in the GnomAD database, including 12,982 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 0.39 (12982 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 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: 0.394 AC: 59852 AN: 151806 Hom.: 12959 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.394 AC: 59916 AN: 151926 Hom.: 12982 Cov.: 31 AF XY: 0.388 AC XY: 28841 AN XY: 74258

African (AFR) AF: 0.583 AC: 24171 AN: 41434

American (AMR) AF: 0.295 AC: 4508 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1501 AN: 3464

East Asian (EAS) AF: 0.189 AC: 975 AN: 5154

South Asian (SAS) AF: 0.472 AC: 2273 AN: 4816

European-Finnish (FIN) AF: 0.294 AC: 3100 AN: 10534

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22325 AN: 67946

Other (OTH) AF: 0.370 AC: 780 AN: 2110

Alfa AF: 0.356 Hom.: 1852

Bravo AF: 0.400

Asia WGS AF: 0.317 AC: 1103 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.55
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs10148587; hg19: chr14-60689160;