13-106191668-T-A

Variant names:

• chr13-106191668-T-A
• rs9301112
• ENST00000754737.1:n.128+22133A>T

Variant summary

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

The ENST00000754737.1(ENSG00000287923):​n.128+22133A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 152,038 control chromosomes in the GnomAD database, including 27,687 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 0.57 (27687 hom., cov: 32)
• Consequence: ENSG00000287923 ENST00000754737.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 3 publications found

Genes affected

ENSG00000287923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754737.1. 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
	ENSG00000287923	ENST00000754737.1		n.128+22133A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87002 AN: 151922 Hom.: 27686 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.572 AC: 87017 AN: 152038 Hom.: 27687 Cov.: 32 AF XY: 0.574 AC XY: 42678 AN XY: 74316

African (AFR) AF: 0.272 AC: 11303 AN: 41492

American (AMR) AF: 0.627 AC: 9555 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2670 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2326 AN: 5180

South Asian (SAS) AF: 0.702 AC: 3384 AN: 4820

European-Finnish (FIN) AF: 0.668 AC: 7055 AN: 10562

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48543 AN: 67966

Other (OTH) AF: 0.607 AC: 1278 AN: 2106

Alfa AF: 0.629 Hom.: 3817

Bravo AF: 0.551

Asia WGS AF: 0.557 AC: 1932 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.20
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs9301112; hg19: chr13-106844017;