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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901056	XR_007058919.1	n.1774+95225T>G		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248752	ENST00000651847.1	n.395+5758T>G		intron_variant	Intron 4 of 15
ENSG00000248752	ENST00000781630.1	n.243+5758T>G		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs13169113; hg19: chr5-125338475;