2-113155116-C-T

Variant names:

• chr2-113155116-C-T
• rs931471

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 0.556 in 152,030 control chromosomes in the GnomAD database, including 25,300 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 0.56 (25300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84413 AN: 151912 Hom.: 25277 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.556 AC: 84467 AN: 152030 Hom.: 25300 Cov.: 32 AF XY: 0.554 AC XY: 41147 AN XY: 74320

African (AFR) AF: 0.369 AC: 15282 AN: 41424

American (AMR) AF: 0.592 AC: 9042 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2541 AN: 3472

East Asian (EAS) AF: 0.171 AC: 887 AN: 5180

South Asian (SAS) AF: 0.754 AC: 3644 AN: 4830

European-Finnish (FIN) AF: 0.578 AC: 6100 AN: 10562

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45052 AN: 67976

Other (OTH) AF: 0.617 AC: 1300 AN: 2106

Alfa AF: 0.638 Hom.: 16502

Bravo AF: 0.543

Asia WGS AF: 0.503 AC: 1749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.66
DANN	Benign	0.28
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs931471; hg19: chr2-113912693;