10-129014291-A-G

Variant names:

• chr10-129014291-A-G
• rs1869251

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 0.41 in 151,918 control chromosomes in the GnomAD database, including 13,053 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 0.41 (13053 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.459 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: 0.410 AC: 62202 AN: 151800 Hom.: 13048 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.410 AC: 62220 AN: 151918 Hom.: 13053 Cov.: 32 AF XY: 0.406 AC XY: 30156 AN XY: 74236

African (AFR) AF: 0.316 AC: 13116 AN: 41442

American (AMR) AF: 0.448 AC: 6833 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1668 AN: 3470

East Asian (EAS) AF: 0.343 AC: 1760 AN: 5126

South Asian (SAS) AF: 0.300 AC: 1440 AN: 4806

European-Finnish (FIN) AF: 0.413 AC: 4347 AN: 10528

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31499 AN: 67986

Other (OTH) AF: 0.435 AC: 917 AN: 2110

Alfa AF: 0.444 Hom.: 46580

Bravo AF: 0.411

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.89
DANN	Benign	0.45
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs1869251; hg19: chr10-130812555;