rs2195499

Variant names:

• chr2-41639259-A-G
• rs2195499

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 0.189 in 152,158 control chromosomes in the GnomAD database, including 2,796 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 (2796 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.214 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: 0.189 AC: 28709 AN: 152038 Hom.: 2792 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.112

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.189 AC: 28743 AN: 152158 Hom.: 2796 Cov.: 32 AF XY: 0.188 AC XY: 13959 AN XY: 74384

African (AFR) AF: 0.146 AC: 6076 AN: 41520

American (AMR) AF: 0.220 AC: 3369 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 647 AN: 3470

East Asian (EAS) AF: 0.216 AC: 1116 AN: 5168

South Asian (SAS) AF: 0.168 AC: 812 AN: 4824

European-Finnish (FIN) AF: 0.184 AC: 1951 AN: 10580

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.208 AC: 14114 AN: 67998

Other (OTH) AF: 0.185 AC: 390 AN: 2110

Alfa AF: 0.210 Hom.: 522

Bravo AF: 0.190

Asia WGS AF: 0.232 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.29
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2195499; hg19: chr2-41866399;