2-138817774-G-A

Variant names:

• chr2-138817774-G-A
• rs4347759

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 0.324 in 151,892 control chromosomes in the GnomAD database, including 8,041 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 0.32 (8041 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.352 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: 0.324 AC: 49247 AN: 151774 Hom.: 8040 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.324 AC: 49270 AN: 151892 Hom.: 8041 Cov.: 32 AF XY: 0.324 AC XY: 24031 AN XY: 74228

African (AFR) AF: 0.303 AC: 12532 AN: 41410

American (AMR) AF: 0.360 AC: 5490 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3466

East Asian (EAS) AF: 0.329 AC: 1699 AN: 5158

South Asian (SAS) AF: 0.279 AC: 1343 AN: 4820

European-Finnish (FIN) AF: 0.325 AC: 3422 AN: 10532

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.331 AC: 22484 AN: 67940

Other (OTH) AF: 0.324 AC: 682 AN: 2106

Alfa AF: 0.330 Hom.: 28234

Bravo AF: 0.326

Asia WGS AF: 0.311 AC: 1078 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs4347759; hg19: chr2-139575344;