13-109484797-G-T

Variant names:

• chr13-109484797-G-T
• rs11620131
• ENST00000650264.1:n.934-5477C>A

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.934-5477C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,002 control chromosomes in the GnomAD database, including 2,256 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 0.15 (2256 hom., cov: 33)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 2 publications found

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650264.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285534	ENST00000650264.1		n.934-5477C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22299 AN: 151884 Hom.: 2260 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.0661

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0951

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.147 AC: 22288 AN: 152002 Hom.: 2256 Cov.: 33 AF XY: 0.146 AC XY: 10814 AN XY: 74300

African (AFR) AF: 0.282 AC: 11669 AN: 41416

American (AMR) AF: 0.0792 AC: 1210 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3472

East Asian (EAS) AF: 0.0724 AC: 375 AN: 5182

South Asian (SAS) AF: 0.204 AC: 981 AN: 4816

European-Finnish (FIN) AF: 0.0661 AC: 697 AN: 10542

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0951 AC: 6464 AN: 67980

Other (OTH) AF: 0.126 AC: 266 AN: 2106

Alfa AF: 0.104 Hom.: 1672

Bravo AF: 0.150

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.086
DANN	Benign	0.24
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11620131;

hg19: chr13-110137144;