rs13028485

chr2-173640196-G-Achr2-173640196-G-Cchr2-173640196-G-T

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 0.0805 in 152,202 control chromosomes in the GnomAD database, including 548 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 0.080 (548 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

ACMG classification

Verdict is Benign. Variant got -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 = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0804 AC: 12221 AN: 152082 Hom.: 546 Cov.: 33

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0822

Gnomad ASJ AF: 0.0694

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0805 AC: 12246 AN: 152202 Hom.: 548 Cov.: 33 AF XY: 0.0809 AC XY: 6018 AN XY: 74424

Gnomad4 AFR AF: 0.0926

Gnomad4 AMR AF: 0.0824

Gnomad4 ASJ AF: 0.0694

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0680

Gnomad4 OTH AF: 0.0806

Alfa AF: 0.0726 Hom.: 556

Bravo AF: 0.0821

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.8
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13028485; hg19: chr2-174504924;