13-20193818-G-T

Variant names:

• chr13-20193818-G-T
• rs9509086
• ENST00000736390.1:n.231+637C>A

Variant summary

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

The ENST00000736390.1(ENSG00000296095):​n.231+637C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 152,058 control chromosomes in the GnomAD database, including 32,845 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 0.60 (32845 hom., cov: 34)
• Consequence: ENSG00000296095 ENST00000736390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84
• Publications: 5 publications found

Genes affected

ENSG00000296095 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736390.1. 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
	ENSG00000296095	ENST00000736390.1		n.231+637C>A		intron	N/A
	ENSG00000296095	ENST00000736391.1		n.454-143C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91768 AN: 151940 Hom.: 32848 Cov.: 34

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.604 AC: 91776 AN: 152058 Hom.: 32845 Cov.: 34 AF XY: 0.608 AC XY: 45200 AN XY: 74346

African (AFR) AF: 0.198 AC: 8230 AN: 41514

American (AMR) AF: 0.599 AC: 9165 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2588 AN: 3470

East Asian (EAS) AF: 0.582 AC: 2980 AN: 5122

South Asian (SAS) AF: 0.845 AC: 4069 AN: 4818

European-Finnish (FIN) AF: 0.841 AC: 8909 AN: 10590

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.790 AC: 53656 AN: 67936

Other (OTH) AF: 0.616 AC: 1303 AN: 2116

Alfa AF: 0.715 Hom.: 75420

Bravo AF: 0.561

Asia WGS AF: 0.710 AC: 2469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.4
DANN	Benign	0.50
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs9509086; hg19: chr13-20767957;