XR_001749919.1:n.158-4166G>A

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.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

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 v4.9

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;