8-81476428-A-G

Variant names:

• chr8-81476428-A-G
• rs7821186
• ENST00000524085.2:n.299-21489A>G

Variant summary

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

The ENST00000524085.2(ENSG00000253374):​n.299-21489A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,950 control chromosomes in the GnomAD database, including 7,720 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 0.25 (7720 hom., cov: 32)
• Consequence: ENSG00000253374 ENST00000524085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 2 publications found

Genes affected

ENSG00000253374 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927118	XR_001745980.2	n.517+14454A>G		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253374	ENST00000524085.2	n.299-21489A>G		intron_variant	Intron 2 of 3	5
ENSG00000253374	ENST00000832857.1	n.326+36335A>G		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832858.1	n.308+36335A>G		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832859.1	n.327+36335A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37750 AN: 151834 Hom.: 7692 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.0987

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.249 AC: 37821 AN: 151950 Hom.: 7720 Cov.: 32 AF XY: 0.247 AC XY: 18342 AN XY: 74286

African (AFR) AF: 0.521 AC: 21561 AN: 41404

American (AMR) AF: 0.213 AC: 3249 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0987 AC: 342 AN: 3464

East Asian (EAS) AF: 0.667 AC: 3430 AN: 5140

South Asian (SAS) AF: 0.123 AC: 594 AN: 4816

European-Finnish (FIN) AF: 0.0876 AC: 928 AN: 10596

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.106 AC: 7197 AN: 67970

Other (OTH) AF: 0.224 AC: 472 AN: 2106

Alfa AF: 0.171 Hom.: 477

Bravo AF: 0.278

Asia WGS AF: 0.391 AC: 1358 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.71
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs7821186; hg19: chr8-82388663;