rs13002573

Variant names:

• chr2-164058698-A-G
• rs13002573
• ENST00000429636.1:n.197-108439T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-164058698-A-G
• chr2-164058698-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429636.1(ENSG00000237844):​n.197-108439T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,156 control chromosomes in the GnomAD database, including 3,505 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 0.20 (3505 hom., cov: 32)
• Consequence: ENSG00000237844 ENST00000429636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

Genes affected

ENSG00000237844 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 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
ENSG00000237844	ENST00000429636.1	n.197-108439T>C		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31167 AN: 152038 Hom.: 3501 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.205 AC: 31179 AN: 152156 Hom.: 3505 Cov.: 32 AF XY: 0.204 AC XY: 15145 AN XY: 74392

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.209

Alfa AF: 0.224 Hom.: 4012

Bravo AF: 0.205

Asia WGS AF: 0.272 AC: 942 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.57
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13002573; hg19: chr2-164915208;