2-112959608-T-C

Variant names:

• chr2-112959608-T-C
• rs13415097

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 0.22 in 151,946 control chromosomes in the GnomAD database, including 4,952 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 0.22 (4952 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 8 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 = 0.414 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: 0.220 AC: 33377 AN: 151830 Hom.: 4946 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.220 AC: 33401 AN: 151946 Hom.: 4952 Cov.: 31 AF XY: 0.212 AC XY: 15710 AN XY: 74276

African (AFR) AF: 0.420 AC: 17358 AN: 41370

American (AMR) AF: 0.159 AC: 2424 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3470

East Asian (EAS) AF: 0.0153 AC: 79 AN: 5180

South Asian (SAS) AF: 0.182 AC: 875 AN: 4808

European-Finnish (FIN) AF: 0.0650 AC: 687 AN: 10576

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.156 AC: 10623 AN: 67946

Other (OTH) AF: 0.209 AC: 441 AN: 2110

Alfa AF: 0.182 Hom.: 530

Bravo AF: 0.234

Asia WGS AF: 0.133 AC: 461 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	3.5
DANN	Benign	0.21
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs13415097; hg19: chr2-113717185;