13-102582819-T-C

Variant names:

• chr13-102582819-T-C
• rs1887355
• ENST00000816787.1:n.344-2145A>G

Variant summary

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

The ENST00000816787.1(ENSG00000276957):​n.344-2145A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,116 control chromosomes in the GnomAD database, including 21,009 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 0.52 (21009 hom., cov: 33)
• Consequence: ENSG00000276957 ENST00000816787.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 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.344-2145A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79686 AN: 152000 Hom.: 21006 Cov.: 33

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.524 AC: 79724 AN: 152116 Hom.: 21009 Cov.: 33 AF XY: 0.525 AC XY: 39039 AN XY: 74346

African (AFR) AF: 0.510 AC: 21175 AN: 41508

American (AMR) AF: 0.465 AC: 7111 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1763 AN: 3472

East Asian (EAS) AF: 0.636 AC: 3286 AN: 5168

South Asian (SAS) AF: 0.484 AC: 2331 AN: 4814

European-Finnish (FIN) AF: 0.556 AC: 5883 AN: 10574

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.535 AC: 36382 AN: 67978

Other (OTH) AF: 0.525 AC: 1109 AN: 2112

Alfa AF: 0.430 Hom.: 1964

Bravo AF: 0.520

Asia WGS AF: 0.554 AC: 1923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.75
DANN	Benign	0.68
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1887355; hg19: chr13-103235169;