rs2928826

Variant names:

• chr8-108601865-C-T
• rs2928826
• ENST00000521504.1:n.170+15127C>T

Variant summary

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

The ENST00000521504.1(ENSG00000253949):​n.170+15127C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,070 control chromosomes in the GnomAD database, including 3,522 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 0.21 (3522 hom., cov: 32)
• Consequence: ENSG00000253949 ENST00000521504.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 5 publications found

Genes affected

ENSG00000253949 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 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
ENSG00000253949	ENST00000521504.1	n.170+15127C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32616 AN: 151952 Hom.: 3522 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.214 AC: 32618 AN: 152070 Hom.: 3522 Cov.: 32 AF XY: 0.213 AC XY: 15849 AN XY: 74316

African (AFR) AF: 0.205 AC: 8499 AN: 41502

American (AMR) AF: 0.210 AC: 3215 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 809 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1416 AN: 5162

South Asian (SAS) AF: 0.157 AC: 755 AN: 4820

European-Finnish (FIN) AF: 0.215 AC: 2270 AN: 10554

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14887 AN: 67962

Other (OTH) AF: 0.199 AC: 419 AN: 2110

Alfa AF: 0.216 Hom.: 15197

Bravo AF: 0.214

Asia WGS AF: 0.204 AC: 708 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.6
DANN	Benign	0.61
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs2928826; hg19: chr8-109614094;