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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.487

Alfa AF: 0.426 Hom.: 30471

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs372139; hg19: chr2-38839323;