13-106191284-C-T

Variant names:

• chr13-106191284-C-T
• rs10492651
• ENST00000754737.1:n.128+22517G>A

Variant summary

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

The ENST00000754737.1(ENSG00000287923):​n.128+22517G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 152,020 control chromosomes in the GnomAD database, including 27,698 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 (27698 hom., cov: 33)
• Consequence: ENSG00000287923 ENST00000754737.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.865
• Publications: 2 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=-0.86).
• 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

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
	ENSG00000287923	ENST00000754737.1		n.128+22517G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87030 AN: 151900 Hom.: 27697 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.573 AC: 87047 AN: 152020 Hom.: 27698 Cov.: 33 AF XY: 0.574 AC XY: 42678 AN XY: 74302

African (AFR) AF: 0.273 AC: 11313 AN: 41466

American (AMR) AF: 0.627 AC: 9557 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2670 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2314 AN: 5152

South Asian (SAS) AF: 0.703 AC: 3392 AN: 4828

European-Finnish (FIN) AF: 0.668 AC: 7070 AN: 10584

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

European-Non Finnish (NFE) AF: 0.714 AC: 48547 AN: 67964

Other (OTH) AF: 0.606 AC: 1279 AN: 2110

Alfa AF: 0.516 Hom.: 1862

Bravo AF: 0.551

Asia WGS AF: 0.557 AC: 1937 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.78
DANN	Benign	0.51
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs10492651; hg19: chr13-106843633;