rs1438029

Variant names:

• chr2-139693639-T-G
• rs1438029

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 0.98 in 152,312 control chromosomes in the GnomAD database, including 73,196 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 0.98 (73196 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.986 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: 0.980 AC: 149198 AN: 152194 Hom.: 73138 Cov.: 32

Gnomad AFR AF: 0.994

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.981

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.962

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

GnomAD4 genome AF: 0.980 AC: 149315 AN: 152312 Hom.: 73196 Cov.: 32 AF XY: 0.981 AC XY: 73066 AN XY: 74476

African (AFR) AF: 0.994 AC: 41338 AN: 41574

American (AMR) AF: 0.961 AC: 14700 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.981 AC: 3405 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5169 AN: 5170

South Asian (SAS) AF: 0.991 AC: 4784 AN: 4828

European-Finnish (FIN) AF: 0.992 AC: 10538 AN: 10620

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 66166 AN: 68040

Other (OTH) AF: 0.963 AC: 2031 AN: 2110

Alfa AF: 0.980 Hom.: 9081

Bravo AF: 0.979

Asia WGS AF: 0.994 AC: 3455 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.45
DANN	Benign	0.53
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1438029; hg19: chr2-140451208;