rs1537473

Variant names:

• chr13-58671029-G-C
• rs1537473
• XR_941985.2:n.115-11730C>G

Your query was ambiguous. Multiple possible variants found:

• chr13-58671029-G-C
• chr13-58671029-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_941985.2(LOC105370219):​n.115-11730C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,582 control chromosomes in the GnomAD database, including 3,237 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 0.19 (3237 hom., cov: 32)
• Consequence: LOC105370219 XR_941985.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571
• Publications: 3 publications found

Genes affected

LOC105370219 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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: 0.190 AC: 28732 AN: 151464 Hom.: 3230 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.190 AC: 28751 AN: 151582 Hom.: 3237 Cov.: 32 AF XY: 0.195 AC XY: 14411 AN XY: 74070

African (AFR) AF: 0.114 AC: 4716 AN: 41450

American (AMR) AF: 0.227 AC: 3451 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 546 AN: 3464

East Asian (EAS) AF: 0.497 AC: 2552 AN: 5136

South Asian (SAS) AF: 0.376 AC: 1810 AN: 4810

European-Finnish (FIN) AF: 0.168 AC: 1770 AN: 10538

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13336 AN: 67686

Other (OTH) AF: 0.201 AC: 423 AN: 2102

Alfa AF: 0.0907 Hom.: 127

Bravo AF: 0.188

Asia WGS AF: 0.391 AC: 1357 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs1537473; hg19: chr13-59245163;