2-101897762-C-G

Variant names:

• chr2-101897762-C-G
• rs1003376

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 0.245 in 152,124 control chromosomes in the GnomAD database, including 5,539 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 0.25 (5539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 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: 0.246 AC: 37326 AN: 152006 Hom.: 5539 Cov.: 32

Gnomad AFR AF: 0.0867

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.245 AC: 37338 AN: 152124 Hom.: 5539 Cov.: 32 AF XY: 0.250 AC XY: 18603 AN XY: 74348

African (AFR) AF: 0.0866 AC: 3594 AN: 41518

American (AMR) AF: 0.289 AC: 4420 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 863 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1248 AN: 5168

South Asian (SAS) AF: 0.160 AC: 771 AN: 4814

European-Finnish (FIN) AF: 0.432 AC: 4568 AN: 10568

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21106 AN: 67984

Other (OTH) AF: 0.249 AC: 526 AN: 2114

Alfa AF: 0.288 Hom.: 931

Bravo AF: 0.230

Asia WGS AF: 0.183 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.42
DANN	Benign	0.57
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1003376; hg19: chr2-102514224; COSMIC: COSV68728351;