rs17412858

Variant names:

• chr13-109600261-A-G
• rs17412858
• ENST00000650264.1:n.759-29103T>C

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.759-29103T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,082 control chromosomes in the GnomAD database, including 6,895 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 0.28 (6895 hom., cov: 32)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 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.759-29103T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41967 AN: 151964 Hom.: 6893 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.276 AC: 41967 AN: 152082 Hom.: 6895 Cov.: 32 AF XY: 0.273 AC XY: 20269 AN XY: 74334

African (AFR) AF: 0.112 AC: 4662 AN: 41500

American (AMR) AF: 0.295 AC: 4502 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1115 AN: 3468

East Asian (EAS) AF: 0.0935 AC: 484 AN: 5178

South Asian (SAS) AF: 0.153 AC: 736 AN: 4820

European-Finnish (FIN) AF: 0.388 AC: 4094 AN: 10562

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25245 AN: 67958

Other (OTH) AF: 0.284 AC: 600 AN: 2110

Alfa AF: 0.318 Hom.: 4945

Bravo AF: 0.266

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.25
DANN	Benign	0.46
PhyloP100		0.36

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: rs17412858;

hg19: chr13-110252608;