rs10150529

Variant names:

• chr14-58584954-T-C
• rs10150529

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 0.279 in 152,138 control chromosomes in the GnomAD database, including 5,915 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 0.28 (5915 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 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: 0.279 AC: 42461 AN: 152020 Hom.: 5908 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.279 AC: 42488 AN: 152138 Hom.: 5915 Cov.: 32 AF XY: 0.280 AC XY: 20791 AN XY: 74356

African (AFR) AF: 0.259 AC: 10754 AN: 41524

American (AMR) AF: 0.256 AC: 3915 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 967 AN: 3470

East Asian (EAS) AF: 0.382 AC: 1978 AN: 5176

South Asian (SAS) AF: 0.346 AC: 1670 AN: 4822

European-Finnish (FIN) AF: 0.288 AC: 3045 AN: 10558

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19258 AN: 67984

Other (OTH) AF: 0.263 AC: 553 AN: 2106

Alfa AF: 0.281 Hom.: 4833

Bravo AF: 0.270

Asia WGS AF: 0.349 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.2
DANN	Benign	0.82
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10150529; hg19: chr14-59051672;