2-20147013-T-G

Variant names:

• chr2-20147013-T-G
• rs981395

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 0.472 in 152,042 control chromosomes in the GnomAD database, including 17,410 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 0.47 (17410 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 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: 0.473 AC: 71796 AN: 151924 Hom.: 17405 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.472 AC: 71831 AN: 152042 Hom.: 17410 Cov.: 32 AF XY: 0.464 AC XY: 34507 AN XY: 74314

African (AFR) AF: 0.545 AC: 22626 AN: 41492

American (AMR) AF: 0.412 AC: 6283 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1598 AN: 3466

East Asian (EAS) AF: 0.224 AC: 1160 AN: 5168

South Asian (SAS) AF: 0.318 AC: 1530 AN: 4816

European-Finnish (FIN) AF: 0.422 AC: 4460 AN: 10568

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32569 AN: 67954

Other (OTH) AF: 0.480 AC: 1016 AN: 2116

Alfa AF: 0.472 Hom.: 36172

Bravo AF: 0.476

Asia WGS AF: 0.290 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.4
DANN	Benign	0.83
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs981395; hg19: chr2-20346774;