rs13028485

Variant names:

• chr2-173640196-G-A
• rs13028485

Your query was ambiguous. Multiple possible variants found:

• chr2-173640196-G-A
• chr2-173640196-G-C
• chr2-173640196-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;