2-113155116-C-T

Variant names:

• chr2-113155116-C-T
• rs931471

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 0.556 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.617

Alfa AF: 0.639 Hom.: 14755

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs931471; hg19: chr2-113912693;