chr8-28197719-G-A

Variant names:

• chr8-28197719-G-A
• rs13268953
• ENST00000842508.1:n.220-15186C>T

Variant summary

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

The ENST00000842508.1(ENSG00000309630):​n.220-15186C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,154 control chromosomes in the GnomAD database, including 24,218 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 0.56 (24218 hom., cov: 33)
• Consequence: ENSG00000309630 ENST00000842508.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572
• Publications: 8 publications found

Genes affected

ENSG00000309630 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 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
ENSG00000309630	ENST00000842508.1	n.220-15186C>T		intron_variant	Intron 1 of 2
ENSG00000309647	ENST00000842774.1	n.508+4165G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85229 AN: 152036 Hom.: 24189 Cov.: 33

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.561 AC: 85300 AN: 152154 Hom.: 24218 Cov.: 33 AF XY: 0.565 AC XY: 42019 AN XY: 74388

African (AFR) AF: 0.487 AC: 20192 AN: 41480

American (AMR) AF: 0.547 AC: 8370 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1722 AN: 3468

East Asian (EAS) AF: 0.617 AC: 3195 AN: 5178

South Asian (SAS) AF: 0.596 AC: 2874 AN: 4820

European-Finnish (FIN) AF: 0.652 AC: 6896 AN: 10582

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40358 AN: 68020

Other (OTH) AF: 0.528 AC: 1113 AN: 2108

Alfa AF: 0.582 Hom.: 110594

Bravo AF: 0.549

Asia WGS AF: 0.627 AC: 2179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.75
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs13268953; hg19: chr8-28055236;