13-75027216-C-T

Variant names:

• chr13-75027216-C-T
• rs1417549
• XR_001749917.1:n.-129G>A

Variant summary

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

The XR_001749917.1(LOC107984620):​n.-129G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,852 control chromosomes in the GnomAD database, including 19,167 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 0.48 (19167 hom., cov: 31)
• Consequence: LOC107984620 XR_001749917.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481
• Publications: 5 publications found

Genes affected

LOC107984620 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984620	XR_001749917.1	n.-129G>A		upstream_gene_variant
LOC107984620	XR_001749918.1	n.-129G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72717 AN: 151734 Hom.: 19170 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.479 AC: 72716 AN: 151852 Hom.: 19167 Cov.: 31 AF XY: 0.478 AC XY: 35475 AN XY: 74194

African (AFR) AF: 0.245 AC: 10158 AN: 41442

American (AMR) AF: 0.546 AC: 8309 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1921 AN: 3470

East Asian (EAS) AF: 0.538 AC: 2764 AN: 5140

South Asian (SAS) AF: 0.428 AC: 2057 AN: 4804

European-Finnish (FIN) AF: 0.587 AC: 6179 AN: 10524

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39552 AN: 67926

Other (OTH) AF: 0.502 AC: 1060 AN: 2110

Alfa AF: 0.543 Hom.: 12515

Bravo AF: 0.469

Asia WGS AF: 0.489 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.9
DANN	Benign	0.70
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs1417549; hg19: chr13-75601353;