13-102584853-G-A

Variant names:

• chr13-102584853-G-A
• rs1887353
• ENST00000816787.1:n.344-4179C>T

Variant summary

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

The ENST00000816787.1(ENSG00000276957):​n.344-4179C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,070 control chromosomes in the GnomAD database, including 32,180 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 0.64 (32180 hom., cov: 32)
• Consequence: ENSG00000276957 ENST00000816787.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 2 publications found

Genes affected

ENSG00000276957 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 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
ENSG00000276957	ENST00000816787.1	n.344-4179C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96911 AN: 151952 Hom.: 32142 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.638 AC: 97004 AN: 152070 Hom.: 32180 Cov.: 32 AF XY: 0.634 AC XY: 47105 AN XY: 74308

African (AFR) AF: 0.842 AC: 34951 AN: 41530

American (AMR) AF: 0.535 AC: 8172 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 2000 AN: 3472

East Asian (EAS) AF: 0.627 AC: 3239 AN: 5164

South Asian (SAS) AF: 0.491 AC: 2365 AN: 4814

European-Finnish (FIN) AF: 0.545 AC: 5739 AN: 10538

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38470 AN: 67974

Other (OTH) AF: 0.631 AC: 1328 AN: 2104

Alfa AF: 0.595 Hom.: 3437

Bravo AF: 0.650

Asia WGS AF: 0.590 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.94
DANN	Benign	0.20
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1887353; hg19: chr13-103237203;