rs13169113

Variant names:

• chr5-126002782-A-C
• rs13169113
• ENST00000651847.1:n.395+5758T>G

Variant summary

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

The ENST00000651847.1(ENSG00000248752):​n.395+5758T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,864 control chromosomes in the GnomAD database, including 13,561 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 0.41 (13561 hom., cov: 31)
• Consequence: ENSG00000248752 ENST00000651847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 4 publications found

Genes affected

ENSG00000248752 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651847.1. 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
	ENSG00000248752	ENST00000651847.1		n.395+5758T>G		intron	N/A
	ENSG00000248752	ENST00000781630.1		n.243+5758T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62384 AN: 151748 Hom.: 13547 Cov.: 31

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.411 AC: 62429 AN: 151864 Hom.: 13561 Cov.: 31 AF XY: 0.411 AC XY: 30525 AN XY: 74180

African (AFR) AF: 0.269 AC: 11147 AN: 41436

American (AMR) AF: 0.430 AC: 6550 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1761 AN: 3466

East Asian (EAS) AF: 0.321 AC: 1656 AN: 5152

South Asian (SAS) AF: 0.439 AC: 2110 AN: 4808

European-Finnish (FIN) AF: 0.499 AC: 5256 AN: 10540

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32481 AN: 67912

Other (OTH) AF: 0.446 AC: 940 AN: 2108

Alfa AF: 0.449 Hom.: 30102

Bravo AF: 0.398

Asia WGS AF: 0.399 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		-0.17

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: rs13169113;

hg19: chr5-125338475;