rs10130259

Variant names:

• chr14-82875978-T-C
• rs10130259

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 0.111 in 152,056 control chromosomes in the GnomAD database, including 1,009 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 0.11 (1009 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 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: 0.111 AC: 16892 AN: 151938 Hom.: 1007 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0478

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.111 AC: 16910 AN: 152056 Hom.: 1009 Cov.: 32 AF XY: 0.108 AC XY: 8027 AN XY: 74334

African (AFR) AF: 0.107 AC: 4451 AN: 41474

American (AMR) AF: 0.0902 AC: 1379 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3472

East Asian (EAS) AF: 0.0479 AC: 247 AN: 5154

South Asian (SAS) AF: 0.0499 AC: 240 AN: 4808

European-Finnish (FIN) AF: 0.102 AC: 1077 AN: 10582

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8611 AN: 67964

Other (OTH) AF: 0.115 AC: 243 AN: 2112

Alfa AF: 0.118 Hom.: 1826

Bravo AF: 0.111

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.64
DANN	Benign	0.60
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10130259; hg19: chr14-83342322;