13-103530140-G-C

Variant names:

• chr13-103530140-G-C
• rs7325773
• ENST00000787871.1:n.427-2531G>C

Variant summary

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

The ENST00000787871.1(ENSG00000302562):​n.427-2531G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 151,920 control chromosomes in the GnomAD database, including 38,875 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 0.70 (38875 hom., cov: 33)
• Consequence: ENSG00000302562 ENST00000787871.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 2 publications found

Genes affected

ENSG00000302562 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302562	ENST00000787871.1	n.427-2531G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.705 AC: 106966 AN: 151802 Hom.: 38860 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.704 AC: 107023 AN: 151920 Hom.: 38875 Cov.: 33 AF XY: 0.698 AC XY: 51791 AN XY: 74224

African (AFR) AF: 0.558 AC: 23119 AN: 41448

American (AMR) AF: 0.818 AC: 12465 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2907 AN: 3470

East Asian (EAS) AF: 0.547 AC: 2801 AN: 5118

South Asian (SAS) AF: 0.699 AC: 3368 AN: 4818

European-Finnish (FIN) AF: 0.589 AC: 6230 AN: 10570

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53817 AN: 67946

Other (OTH) AF: 0.736 AC: 1551 AN: 2108

Alfa AF: 0.636 Hom.: 1792

Bravo AF: 0.718

Asia WGS AF: 0.608 AC: 2119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.087
DANN	Benign	0.46
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7325773; hg19: chr13-104182490;