2-203880101-C-G

Variant names:

• chr2-203880101-C-G
• rs10932025

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 0.176 in 151,954 control chromosomes in the GnomAD database, including 2,470 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 0.18 (2470 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 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: 0.176 AC: 26783 AN: 151836 Hom.: 2464 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.176 AC: 26813 AN: 151954 Hom.: 2470 Cov.: 31 AF XY: 0.174 AC XY: 12891 AN XY: 74256

African (AFR) AF: 0.163 AC: 6769 AN: 41422

American (AMR) AF: 0.147 AC: 2252 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3472

East Asian (EAS) AF: 0.117 AC: 603 AN: 5170

South Asian (SAS) AF: 0.0990 AC: 476 AN: 4810

European-Finnish (FIN) AF: 0.160 AC: 1686 AN: 10544

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13693 AN: 67954

Other (OTH) AF: 0.183 AC: 386 AN: 2110

Alfa AF: 0.186 Hom.: 348

Bravo AF: 0.176

Asia WGS AF: 0.112 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.2
DANN	Benign	0.76
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10932025; hg19: chr2-204744824;