8-82696337-A-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986953	XR_001745983.1	n.84-526A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254394	ENST00000658531.1	n.253+92707A>T		intron_variant	Intron 3 of 3
ENSG00000254394	ENST00000663058.1	n.943+92707A>T		intron_variant	Intron 6 of 7

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 v4.3

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

Other links and lift over

dbSNP: rs7812601; hg19: chr8-83608572;