13-59532791-T-C

Variant names:

• chr13-59532791-T-C
• rs1622710
• XR_001749886.2:n.234-1403A>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.234-1403A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,146 control chromosomes in the GnomAD database, including 47,838 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 0.74 (47838 hom., cov: 33)
• Consequence: LOC107984625 XR_001749886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.737 AC: 112007 AN: 152030 Hom.: 47835 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.736 AC: 112014 AN: 152146 Hom.: 47838 Cov.: 33 AF XY: 0.739 AC XY: 54995 AN XY: 74398

African (AFR) AF: 0.267 AC: 11073 AN: 41468

American (AMR) AF: 0.846 AC: 12930 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2974 AN: 3468

East Asian (EAS) AF: 0.793 AC: 4097 AN: 5164

South Asian (SAS) AF: 0.838 AC: 4047 AN: 4828

European-Finnish (FIN) AF: 0.926 AC: 9813 AN: 10600

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64395 AN: 68016

Other (OTH) AF: 0.774 AC: 1633 AN: 2110

Alfa AF: 0.863 Hom.: 99179

Bravo AF: 0.709

Asia WGS AF: 0.794 AC: 2757 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.36
DANN	Benign	0.67
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1622710; hg19: chr13-60106925;