2-138868291-T-G

Variant names:

• chr2-138868291-T-G
• rs936762

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 0.679 in 152,092 control chromosomes in the GnomAD database, including 35,152 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 0.68 (35152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.703 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: 0.679 AC: 103201 AN: 151974 Hom.: 35111 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.679 AC: 103301 AN: 152092 Hom.: 35152 Cov.: 32 AF XY: 0.680 AC XY: 50526 AN XY: 74344

African (AFR) AF: 0.710 AC: 29446 AN: 41484

American (AMR) AF: 0.644 AC: 9841 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2289 AN: 3468

East Asian (EAS) AF: 0.672 AC: 3475 AN: 5170

South Asian (SAS) AF: 0.722 AC: 3483 AN: 4822

European-Finnish (FIN) AF: 0.675 AC: 7121 AN: 10550

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.668 AC: 45455 AN: 67996

Other (OTH) AF: 0.677 AC: 1427 AN: 2108

Alfa AF: 0.604 Hom.: 3025

Bravo AF: 0.678

Asia WGS AF: 0.687 AC: 2392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs936762; hg19: chr2-139625861;