rs13415097

chr2-112959608-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.0153

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.0650

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.209

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.5
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13415097; hg19: chr2-113717185;