chr2-138817774-G-A

Variant names:

• chr2-138817774-G-A
• rs4347759

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 0.324 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.324

Alfa AF: 0.331 Hom.: 17483

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4347759; hg19: chr2-139575344;