rs13403026

Variant names:

• chr2-126860860-G-A
• rs13403026

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 0.0504 in 152,282 control chromosomes in the GnomAD database, including 250 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 0.050 (250 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.102 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: 0.0504 AC: 7663 AN: 152164 Hom.: 249 Cov.: 33

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0349

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.0586

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0242

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0383

Gnomad OTH AF: 0.0489

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

GnomAD4 genome AF: 0.0504 AC: 7669 AN: 152282 Hom.: 250 Cov.: 33 AF XY: 0.0499 AC XY: 3716 AN XY: 74464

African (AFR) AF: 0.0741 AC: 3079 AN: 41564

American (AMR) AF: 0.0349 AC: 534 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3470

East Asian (EAS) AF: 0.0586 AC: 304 AN: 5190

South Asian (SAS) AF: 0.110 AC: 528 AN: 4818

European-Finnish (FIN) AF: 0.0242 AC: 257 AN: 10604

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0384 AC: 2609 AN: 68014

Other (OTH) AF: 0.0484 AC: 102 AN: 2108

Alfa AF: 0.0423 Hom.: 23

Bravo AF: 0.0506

Asia WGS AF: 0.0880 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.53
DANN	Benign	0.48
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs13403026; hg19: chr2-127618436;