rs1869251

chr10-129014291-A-Gchr10-129014291-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.435

Alfa AF: 0.452 Hom.: 30365

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1869251; hg19: chr10-130812555;