13-98134278-T-C

Variant names:

• chr13-98134278-T-C
• rs285032
• ENST00000717002.1:n.116+9561A>G

Variant summary

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

The ENST00000717002.1(ENSG00000293659):​n.116+9561A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 148,220 control chromosomes in the GnomAD database, including 24,092 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 0.57 (24092 hom., cov: 26)
• Consequence: ENSG00000293659 ENST00000717002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 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+9561A>G		intron	N/A
	ENSG00000293659	ENST00000717003.1		n.90+9561A>G		intron	N/A
	ENSG00000293659	ENST00000717004.1		n.51+9561A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.565 AC: 83668 AN: 148112 Hom.: 24037 Cov.: 26

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.590

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.565 AC: 83773 AN: 148220 Hom.: 24092 Cov.: 26 AF XY: 0.573 AC XY: 41263 AN XY: 72036

African (AFR) AF: 0.691 AC: 28079 AN: 40630

American (AMR) AF: 0.622 AC: 9131 AN: 14686

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1768 AN: 3426

East Asian (EAS) AF: 0.576 AC: 2883 AN: 5006

South Asian (SAS) AF: 0.639 AC: 2938 AN: 4596

European-Finnish (FIN) AF: 0.517 AC: 4918 AN: 9520

Middle Eastern (MID) AF: 0.607 AC: 176 AN: 290

European-Non Finnish (NFE) AF: 0.482 AC: 32367 AN: 67126

Other (OTH) AF: 0.556 AC: 1137 AN: 2044

Alfa AF: 0.526 Hom.: 9471

Bravo AF: 0.573

Asia WGS AF: 0.575 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.77
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs285032; hg19: chr13-98786532;