2-58417312-A-G

Variant names:

• chr2-58417312-A-G
• rs35267016

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 0.11 in 152,204 control chromosomes in the GnomAD database, including 1,073 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 0.11 (1073 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 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: 0.110 AC: 16762 AN: 152086 Hom.: 1075 Cov.: 32

Gnomad AFR AF: 0.0458

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.110 AC: 16769 AN: 152204 Hom.: 1073 Cov.: 32 AF XY: 0.112 AC XY: 8338 AN XY: 74416

African (AFR) AF: 0.0459 AC: 1905 AN: 41542

American (AMR) AF: 0.143 AC: 2194 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3470

East Asian (EAS) AF: 0.161 AC: 833 AN: 5172

South Asian (SAS) AF: 0.195 AC: 936 AN: 4804

European-Finnish (FIN) AF: 0.131 AC: 1388 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8676 AN: 68006

Other (OTH) AF: 0.137 AC: 290 AN: 2112

Alfa AF: 0.0741 Hom.: 107

Bravo AF: 0.111

Asia WGS AF: 0.198 AC: 685 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	7.4
DANN	Benign	0.61
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs35267016; hg19: chr2-58644447;