8-131292261-T-C

Variant names:

• chr8-131292261-T-C
• rs10102742
• ENST00000745605.1:n.282+20327A>G

Variant summary

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

The ENST00000745605.1(ENSG00000297116):​n.282+20327A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,230 control chromosomes in the GnomAD database, including 27,960 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 0.60 (27960 hom., cov: 29)
• Consequence: ENSG00000297116 ENST00000745605.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 1 publications found

Genes affected

ENSG00000297116 (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 (AFR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745605.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297116	ENST00000745605.1		n.282+20327A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91253 AN: 151114 Hom.: 27928 Cov.: 29

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.604 AC: 91342 AN: 151230 Hom.: 27960 Cov.: 29 AF XY: 0.596 AC XY: 44055 AN XY: 73908

African (AFR) AF: 0.703 AC: 29020 AN: 41280

American (AMR) AF: 0.516 AC: 7799 AN: 15122

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1814 AN: 3460

East Asian (EAS) AF: 0.398 AC: 2047 AN: 5148

South Asian (SAS) AF: 0.539 AC: 2579 AN: 4782

European-Finnish (FIN) AF: 0.555 AC: 5792 AN: 10442

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40424 AN: 67692

Other (OTH) AF: 0.559 AC: 1174 AN: 2100

Alfa AF: 0.594 Hom.: 83225

Bravo AF: 0.601

Asia WGS AF: 0.463 AC: 1610 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.70
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10102742; hg19: chr8-132304508;