rs1146904

Variant names:

• chr13-76521501-G-A
• rs1146904
• XR_001749919.1:n.158-4166G>A

Variant summary

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

The XR_001749919.1(LOC105370263):​n.158-4166G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,960 control chromosomes in the GnomAD database, including 22,196 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 0.54 (22196 hom., cov: 32)
• Consequence: LOC105370263 XR_001749919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561
• Publications: 0 publications found

Genes affected

LOC105370263 (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 (AMR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370263	XR_001749919.1	n.158-4166G>A		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81551 AN: 151840 Hom.: 22169 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.537 AC: 81617 AN: 151960 Hom.: 22196 Cov.: 32 AF XY: 0.538 AC XY: 39962 AN XY: 74236

African (AFR) AF: 0.548 AC: 22713 AN: 41414

American (AMR) AF: 0.659 AC: 10059 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1868 AN: 3468

East Asian (EAS) AF: 0.476 AC: 2452 AN: 5150

South Asian (SAS) AF: 0.594 AC: 2865 AN: 4820

European-Finnish (FIN) AF: 0.444 AC: 4693 AN: 10558

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35055 AN: 67966

Other (OTH) AF: 0.569 AC: 1201 AN: 2110

Alfa AF: 0.524 Hom.: 11081

Bravo AF: 0.554

Asia WGS AF: 0.536 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.10
DANN	Benign	0.76
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1146904; hg19: chr13-77095636;