rs13169113

Positions:

• chr5-126002782-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651847.1(ENSG00000248752):​n.395+5758T>G variant causes a intron, non coding transcript 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: ENST00000651847.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124901056	XR_007058919.1	n.1774+95225T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651847.1	n.395+5758T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.446

Alfa AF: 0.462 Hom.: 8997

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13169113; hg19: chr5-125338475;