chr2-113135197-A-G

Variant names:

• chr2-113135197-A-G
• rs315949

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 0.635 in 152,044 control chromosomes in the GnomAD database, including 31,227 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 0.64 (31227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 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: 0.635 AC: 96474 AN: 151926 Hom.: 31184 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.635 AC: 96563 AN: 152044 Hom.: 31227 Cov.: 32 AF XY: 0.640 AC XY: 47514 AN XY: 74298

African (AFR) AF: 0.650 AC: 26972 AN: 41466

American (AMR) AF: 0.682 AC: 10424 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1860 AN: 3470

East Asian (EAS) AF: 0.924 AC: 4779 AN: 5174

South Asian (SAS) AF: 0.519 AC: 2498 AN: 4816

European-Finnish (FIN) AF: 0.702 AC: 7415 AN: 10560

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40702 AN: 67974

Other (OTH) AF: 0.604 AC: 1274 AN: 2110

Alfa AF: 0.625 Hom.: 11400

Bravo AF: 0.637

Asia WGS AF: 0.703 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.40
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs315949; hg19: chr2-113892774; COSMIC: COSV52080191;