rs10197010

Variant names:

• chr2-203875448-A-C
• rs10197010

Your query was ambiguous. Multiple possible variants found:

• chr2-203875448-A-C
• chr2-203875448-A-G
• chr2-203875448-A-T

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 0.185 in 152,200 control chromosomes in the GnomAD database, including 2,695 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 0.19 (2695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 9 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 (AFR) allele frequency at 95% confidence interval = 0.201 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: 0.185 AC: 28133 AN: 152082 Hom.: 2690 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0983

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.185 AC: 28167 AN: 152200 Hom.: 2695 Cov.: 32 AF XY: 0.182 AC XY: 13543 AN XY: 74406

African (AFR) AF: 0.205 AC: 8498 AN: 41520

American (AMR) AF: 0.143 AC: 2192 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 707 AN: 3470

East Asian (EAS) AF: 0.126 AC: 655 AN: 5184

South Asian (SAS) AF: 0.0996 AC: 480 AN: 4820

European-Finnish (FIN) AF: 0.165 AC: 1748 AN: 10596

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13246 AN: 68000

Other (OTH) AF: 0.189 AC: 399 AN: 2110

Alfa AF: 0.161 Hom.: 883

Bravo AF: 0.187

Asia WGS AF: 0.119 AC: 416 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	0.024
DANN	Benign	0.72
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs10197010; hg19: chr2-204740171;