rs10915029

Variant names:

• chr1-30106075-C-T
• rs10915029

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 0.468 in 152,042 control chromosomes in the GnomAD database, including 17,429 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 0.47 (17429 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.831

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 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: 0.468 AC: 71074 AN: 151924 Hom.: 17422 Cov.: 33

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.468 AC: 71111 AN: 152042 Hom.: 17429 Cov.: 33 AF XY: 0.473 AC XY: 35157 AN XY: 74308

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.490

Alfa AF: 0.500 Hom.: 19018

Bravo AF: 0.462

Asia WGS AF: 0.629 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10915029; hg19: chr1-30578922; COSMIC: COSV59935055;