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 ENST00000832857.1(ENSG00000253374):​n.326+36335A>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 ENST00000832857.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832857.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253374	ENST00000524085.2	TSL:5	n.299-21489A>G		intron	N/A
	ENSG00000253374	ENST00000832857.1		n.326+36335A>G		intron	N/A
	ENSG00000253374	ENST00000832858.1		n.308+36335A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7821186;

hg19: chr8-82388663;