13-59541970-T-C

Variant names:

• chr13-59541970-T-C
• rs831223
• XR_001749886.2:n.234-10582A>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.234-10582A>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 152,156 control chromosomes in the GnomAD database, including 47,793 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 (47793 hom., cov: 32)
• Consequence: LOC107984625 XR_001749886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.938 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: 0.737 AC: 112016 AN: 152038 Hom.: 47784 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.736 AC: 112033 AN: 152156 Hom.: 47793 Cov.: 32 AF XY: 0.740 AC XY: 55035 AN XY: 74390

African (AFR) AF: 0.270 AC: 11181 AN: 41468

American (AMR) AF: 0.843 AC: 12893 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2977 AN: 3470

East Asian (EAS) AF: 0.792 AC: 4094 AN: 5166

South Asian (SAS) AF: 0.890 AC: 4287 AN: 4818

European-Finnish (FIN) AF: 0.916 AC: 9715 AN: 10608

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.944 AC: 64205 AN: 68008

Other (OTH) AF: 0.772 AC: 1634 AN: 2116

Alfa AF: 0.880 Hom.: 100534

Bravo AF: 0.710

Asia WGS AF: 0.798 AC: 2778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.81
DANN	Benign	0.58
PhyloP100		-0.082

Splicing

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

Other links and lift over

dbSNP: rs831223; hg19: chr13-60116104;