10-99872112-C-T

Variant names:

• chr10-99872112-C-T
• rs2862919

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 0.372 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.270 AC: 11183 AN: 41448

American (AMR) AF: 0.399 AC: 6095 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1432 AN: 3466

East Asian (EAS) AF: 0.235 AC: 1212 AN: 5168

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4820

European-Finnish (FIN) AF: 0.361 AC: 3810 AN: 10552

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29494 AN: 67980

Other (OTH) AF: 0.408 AC: 859 AN: 2106

Alfa AF: 0.414 Hom.: 6974

Bravo AF: 0.371

Asia WGS AF: 0.309 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.68
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2862919; hg19: chr10-101631869;