rs13028041

Variant names:

• chr2-118120458-A-G
• rs13028041

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 0.253 in 152,100 control chromosomes in the GnomAD database, including 5,355 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 0.25 (5355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 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: 0.253 AC: 38432 AN: 151982 Hom.: 5351 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.253 AC: 38453 AN: 152100 Hom.: 5355 Cov.: 32 AF XY: 0.251 AC XY: 18671 AN XY: 74358

African (AFR) AF: 0.136 AC: 5629 AN: 41510

American (AMR) AF: 0.311 AC: 4754 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3470

East Asian (EAS) AF: 0.392 AC: 2018 AN: 5154

South Asian (SAS) AF: 0.320 AC: 1544 AN: 4822

European-Finnish (FIN) AF: 0.235 AC: 2490 AN: 10596

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20165 AN: 67964

Other (OTH) AF: 0.251 AC: 530 AN: 2110

Alfa AF: 0.277 Hom.: 11063

Bravo AF: 0.254

Asia WGS AF: 0.315 AC: 1095 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.088
DANN	Benign	0.45
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs13028041; hg19: chr2-118878034;