13-59541970-T-C

Variant names:

• chr13-59541970-T-C
• rs831223
• XR_001749886.2:n.234-10582A>G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC107984625 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984625	XR_001749886.2	n.234-10582A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.890

Gnomad4 FIN AF: 0.916

Gnomad4 NFE AF: 0.944

Gnomad4 OTH AF: 0.772

Alfa AF: 0.900 Hom.: 81719

Bravo AF: 0.710

Asia WGS AF: 0.798 AC: 2778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs831223; hg19: chr13-60116104;