2-204116194-C-T

Variant names:

• chr2-204116194-C-T
• rs10195135

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 0.297 in 151,922 control chromosomes in the GnomAD database, including 8,921 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 0.30 (8921 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45057 AN: 151804 Hom.: 8897 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.297 AC: 45128 AN: 151922 Hom.: 8921 Cov.: 32 AF XY: 0.296 AC XY: 21958 AN XY: 74266

African (AFR) AF: 0.548 AC: 22657 AN: 41328

American (AMR) AF: 0.311 AC: 4743 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 865 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1545 AN: 5168

South Asian (SAS) AF: 0.321 AC: 1543 AN: 4810

European-Finnish (FIN) AF: 0.0975 AC: 1033 AN: 10592

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11977 AN: 67986

Other (OTH) AF: 0.264 AC: 556 AN: 2106

Alfa AF: 0.212 Hom.: 2206

Bravo AF: 0.322

Asia WGS AF: 0.348 AC: 1208 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	0.64
DANN	Benign	0.41
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10195135; hg19: chr2-204980917; COSMIC: COSV107166328;