chr8-81452940-T-A

Variant names:

• chr8-81452940-T-A
• rs7835371
• ENST00000524085.2:n.298+12847T>A

Variant summary

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

The ENST00000832857.1(ENSG00000253374):​n.326+12847T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,102 control chromosomes in the GnomAD database, including 5,180 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 0.23 (5180 hom., cov: 32)
• Consequence: ENSG00000253374 ENST00000832857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 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.298+12847T>A		intron	N/A
	ENSG00000253374	ENST00000832857.1		n.326+12847T>A		intron	N/A
	ENSG00000253374	ENST00000832858.1		n.308+12847T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34561 AN: 151984 Hom.: 5178 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0821

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.227 AC: 34589 AN: 152102 Hom.: 5180 Cov.: 32 AF XY: 0.225 AC XY: 16705 AN XY: 74378

African (AFR) AF: 0.312 AC: 12925 AN: 41466

American (AMR) AF: 0.268 AC: 4088 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3466

East Asian (EAS) AF: 0.738 AC: 3813 AN: 5170

South Asian (SAS) AF: 0.183 AC: 882 AN: 4826

European-Finnish (FIN) AF: 0.0821 AC: 872 AN: 10616

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10852 AN: 67976

Other (OTH) AF: 0.237 AC: 501 AN: 2110

Alfa AF: 0.0685 Hom.: 65

Bravo AF: 0.253

Asia WGS AF: 0.435 AC: 1514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.6
DANN	Benign	0.73
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs7835371; hg19: chr8-82365175;