2-49817286-G-A

Variant names:

• chr2-49817286-G-A
• rs17795358

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 0.12 in 152,064 control chromosomes in the GnomAD database, including 1,244 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 0.12 (1244 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18251 AN: 151946 Hom.: 1243 Cov.: 32

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.120 AC: 18249 AN: 152064 Hom.: 1244 Cov.: 32 AF XY: 0.117 AC XY: 8717 AN XY: 74330

African (AFR) AF: 0.0917 AC: 3804 AN: 41464

American (AMR) AF: 0.113 AC: 1722 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5168

South Asian (SAS) AF: 0.0677 AC: 326 AN: 4814

European-Finnish (FIN) AF: 0.121 AC: 1285 AN: 10582

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10138 AN: 67968

Other (OTH) AF: 0.126 AC: 266 AN: 2114

Alfa AF: 0.140 Hom.: 1757

Bravo AF: 0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.69
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs17795358; hg19: chr2-50044424;