ENST00000658531.1:n.253+92707A>T

Variant names:

• chr8-82696337-A-T
• rs7812601
• ENST00000658531.1:n.253+92707A>T

Variant summary

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

The ENST00000658531.1(ENSG00000254394):​n.253+92707A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,178 control chromosomes in the GnomAD database, including 1,407 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 0.13 (1407 hom., cov: 32)
• Consequence: ENSG00000254394 ENST00000658531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 0 publications found

Genes affected

ENSG00000254394 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658531.1. 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
	ENSG00000254394	ENST00000658531.1		n.253+92707A>T		intron	N/A
	ENSG00000254394	ENST00000663058.1		n.943+92707A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20052 AN: 152060 Hom.: 1410 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0984

Gnomad EAS AF: 0.00673

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.132 AC: 20051 AN: 152178 Hom.: 1407 Cov.: 32 AF XY: 0.132 AC XY: 9813 AN XY: 74412

African (AFR) AF: 0.132 AC: 5466 AN: 41504

American (AMR) AF: 0.117 AC: 1793 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0984 AC: 341 AN: 3464

East Asian (EAS) AF: 0.00656 AC: 34 AN: 5186

South Asian (SAS) AF: 0.207 AC: 999 AN: 4826

European-Finnish (FIN) AF: 0.144 AC: 1525 AN: 10598

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9490 AN: 67994

Other (OTH) AF: 0.146 AC: 308 AN: 2112

Alfa AF: 0.0599 Hom.: 62

Bravo AF: 0.129

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.59
PhyloP100		0.30

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: rs7812601;

hg19: chr8-83608572;