rs372139

Variant names:

• chr2-38612181-G-A
• rs372139

Your query was ambiguous. Multiple possible variants found:

• chr2-38612181-G-A
• chr2-38612181-G-C
• chr2-38612181-G-T

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 0.504 in 151,944 control chromosomes in the GnomAD database, including 20,385 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 0.50 (20385 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 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: 0.503 AC: 76409 AN: 151826 Hom.: 20332 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.504 AC: 76517 AN: 151944 Hom.: 20385 Cov.: 32 AF XY: 0.506 AC XY: 37556 AN XY: 74230

African (AFR) AF: 0.649 AC: 26909 AN: 41440

American (AMR) AF: 0.613 AC: 9372 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1556 AN: 3468

East Asian (EAS) AF: 0.715 AC: 3699 AN: 5170

South Asian (SAS) AF: 0.467 AC: 2254 AN: 4824

European-Finnish (FIN) AF: 0.396 AC: 4164 AN: 10514

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27065 AN: 67936

Other (OTH) AF: 0.487 AC: 1026 AN: 2108

Alfa AF: 0.439 Hom.: 69710

Bravo AF: 0.530

Asia WGS AF: 0.596 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.61
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs372139; hg19: chr2-38839323;