rs285031

Variant names:

• chr13-98133777-C-G
• rs285031
• ENST00000717002.1:n.116+10062G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000717002.1(ENSG00000293659):​n.116+10062G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,238 control chromosomes in the GnomAD database, including 2,016 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 0.16 (2016 hom., cov: 32)
• Consequence: ENSG00000293659 ENST00000717002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 3 publications found

Genes affected

ENSG00000293659 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717002.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293659	ENST00000717002.1		n.116+10062G>C		intron	N/A
	ENSG00000293659	ENST00000717003.1		n.90+10062G>C		intron	N/A
	ENSG00000293659	ENST00000717004.1		n.51+10062G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23598 AN: 152120 Hom.: 2016 Cov.: 32

Gnomad AFR AF: 0.0981

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0664

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.155 AC: 23617 AN: 152238 Hom.: 2016 Cov.: 32 AF XY: 0.157 AC XY: 11649 AN XY: 74432

African (AFR) AF: 0.0980 AC: 4071 AN: 41532

American (AMR) AF: 0.215 AC: 3293 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3472

East Asian (EAS) AF: 0.0663 AC: 344 AN: 5186

South Asian (SAS) AF: 0.135 AC: 652 AN: 4830

European-Finnish (FIN) AF: 0.175 AC: 1859 AN: 10598

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12543 AN: 68014

Other (OTH) AF: 0.161 AC: 339 AN: 2112

Alfa AF: 0.161 Hom.: 251

Bravo AF: 0.156

Asia WGS AF: 0.0930 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.63
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs285031; hg19: chr13-98786031;