2-138868291-T-G

Variant names:

• chr2-138868291-T-G
• rs936762

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 0.679 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.677

Alfa AF: 0.598 Hom.: 2821

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs936762; hg19: chr2-139625861;