rs13031008

Variant names:

• chr2-177612386-G-A
• rs13031008
• ENST00000357045.4:n.86-4915G>A

Variant summary

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

The ENST00000357045.4(ENSG00000237655):​n.86-4915G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,024 control chromosomes in the GnomAD database, including 33,354 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 0.64 (33354 hom., cov: 32)
• Consequence: ENSG00000237655 ENST00000357045.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

ENSG00000237655 (HGNC:58181):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.745 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
ENSG00000237655	ENST00000357045.4	n.86-4915G>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97144 AN: 151906 Hom.: 33341 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.639 AC: 97179 AN: 152024 Hom.: 33354 Cov.: 32 AF XY: 0.644 AC XY: 47890 AN XY: 74306

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.742

Gnomad4 OTH AF: 0.655

Alfa AF: 0.720 Hom.: 51869

Bravo AF: 0.623

Asia WGS AF: 0.666 AC: 2315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13031008; hg19: chr2-178477114;