rs2928826

Positions:

• chr8-108601865-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521504.1(ENSG00000253949):​n.170+15127C>T variant causes a intron, non coding transcript 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: ENST00000521504.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000521504.1	n.170+15127C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.199

Alfa AF: 0.217 Hom.: 7382

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2928826; hg19: chr8-109614094;