2-112771606-C-T

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 0.693 in 151,840 control chromosomes in the GnomAD database, including 37,237 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 0.69 (37237 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 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: 0.693 AC: 105179 AN: 151722 Hom.: 37197 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.693 AC: 105261 AN: 151840 Hom.: 37237 Cov.: 31 AF XY: 0.685 AC XY: 50805 AN XY: 74204

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.680

Alfa AF: 0.682 Hom.: 42019

Bravo AF: 0.691

Asia WGS AF: 0.519 AC: 1800 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.8
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6542095; hg19: chr2-113529183;