2-113965225-G-T

Variant names:

• chr2-113965225-G-T
• rs12711793

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 0.385 in 151,948 control chromosomes in the GnomAD database, including 15,492 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 0.38 (15492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 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: 0.385 AC: 58386 AN: 151830 Hom.: 15446 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.385 AC: 58493 AN: 151948 Hom.: 15492 Cov.: 32 AF XY: 0.381 AC XY: 28264 AN XY: 74268

African (AFR) AF: 0.748 AC: 31009 AN: 41448

American (AMR) AF: 0.271 AC: 4139 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 536 AN: 3468

East Asian (EAS) AF: 0.574 AC: 2968 AN: 5168

South Asian (SAS) AF: 0.336 AC: 1616 AN: 4816

European-Finnish (FIN) AF: 0.229 AC: 2417 AN: 10538

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.220 AC: 14920 AN: 67936

Other (OTH) AF: 0.332 AC: 702 AN: 2112

Alfa AF: 0.254 Hom.: 15635

Bravo AF: 0.407

Asia WGS AF: 0.454 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.22
DANN	Benign	0.51
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs12711793; hg19: chr2-114722802;