rs13031008

Positions:

• chr2-177612386-G-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, non coding transcript 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: ENST00000357045.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000357045.4	n.86-4915G>A		intron_variant, non_coding_transcript_variant		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;