10-99872112-C-T

Variant names:

• chr10-99872112-C-T
• rs2862919

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 0.372 in 152,030 control chromosomes in the GnomAD database, including 11,111 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 0.37 (11111 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 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: 0.372 AC: 56463 AN: 151912 Hom.: 11101 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.372 AC: 56523 AN: 152030 Hom.: 11111 Cov.: 32 AF XY: 0.370 AC XY: 27498 AN XY: 74308

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.408

Alfa AF: 0.415 Hom.: 6217

Bravo AF: 0.371

Asia WGS AF: 0.309 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2862919; hg19: chr10-101631869;