2-139390262-C-T

Variant names:

• chr2-139390262-C-T
• rs1399645

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 0.0952 in 151,962 control chromosomes in the GnomAD database, including 988 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 0.095 (988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 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: 0.0953 AC: 14468 AN: 151844 Hom.: 992 Cov.: 32

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0977

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.0474

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0841

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0952 AC: 14469 AN: 151962 Hom.: 988 Cov.: 32 AF XY: 0.0994 AC XY: 7383 AN XY: 74240

African (AFR) AF: 0.0680 AC: 2818 AN: 41444

American (AMR) AF: 0.105 AC: 1593 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0977 AC: 339 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1713 AN: 5154

South Asian (SAS) AF: 0.308 AC: 1481 AN: 4812

European-Finnish (FIN) AF: 0.0474 AC: 501 AN: 10562

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0841 AC: 5717 AN: 67978

Other (OTH) AF: 0.101 AC: 213 AN: 2108

Alfa AF: 0.0966 Hom.: 1952

Bravo AF: 0.0952

Asia WGS AF: 0.313 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.4
DANN	Benign	0.38
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1399645; hg19: chr2-140147832;