chr13-59520528-T-C

Variant names:

• chr13-59520528-T-C
• rs10507632
• XR_001749886.2:n.358-783A>G

Variant summary

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

The XR_001749886.2(LOC107984625):​n.358-783A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,240 control chromosomes in the GnomAD database, including 2,016 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 0.11 (2016 hom., cov: 32)
• Consequence: LOC107984625 XR_001749886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 0 publications found

Genes affected

LOC107984625 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 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: 0.111 AC: 16917 AN: 152122 Hom.: 2012 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0707

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00673

Gnomad SAS AF: 0.0695

Gnomad FIN AF: 0.0340

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0306

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.111 AC: 16937 AN: 152240 Hom.: 2016 Cov.: 32 AF XY: 0.109 AC XY: 8123 AN XY: 74464

African (AFR) AF: 0.297 AC: 12333 AN: 41500

American (AMR) AF: 0.0704 AC: 1077 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3468

East Asian (EAS) AF: 0.00675 AC: 35 AN: 5186

South Asian (SAS) AF: 0.0689 AC: 333 AN: 4834

European-Finnish (FIN) AF: 0.0340 AC: 361 AN: 10614

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0306 AC: 2084 AN: 68020

Other (OTH) AF: 0.108 AC: 228 AN: 2108

Alfa AF: 0.0699 Hom.: 677

Bravo AF: 0.122

Asia WGS AF: 0.0570 AC: 198 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.0
DANN	Benign	0.91
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs10507632; hg19: chr13-60094662;