2-185001013-T-G

Variant names:

• chr2-185001013-T-G
• rs12477914

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 0.137 in 152,104 control chromosomes in the GnomAD database, including 1,963 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 0.14 (1963 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 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: 0.138 AC: 20903 AN: 151986 Hom.: 1960 Cov.: 32

Gnomad AFR AF: 0.0361

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.137 AC: 20910 AN: 152104 Hom.: 1963 Cov.: 32 AF XY: 0.144 AC XY: 10707 AN XY: 74356

African (AFR) AF: 0.0360 AC: 1496 AN: 41548

American (AMR) AF: 0.254 AC: 3873 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1820 AN: 5132

South Asian (SAS) AF: 0.139 AC: 670 AN: 4826

European-Finnish (FIN) AF: 0.206 AC: 2178 AN: 10598

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9828 AN: 67964

Other (OTH) AF: 0.149 AC: 316 AN: 2114

Alfa AF: 0.138 Hom.: 4736

Bravo AF: 0.139

Asia WGS AF: 0.220 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.2
DANN	Benign	0.76
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs12477914; hg19: chr2-185865740;