13-106065154-G-A

Variant names:

• chr13-106065154-G-A
• rs16968122
• ENST00000754737.1:n.415+25354C>T

Variant summary

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

The ENST00000754737.1(ENSG00000287923):​n.415+25354C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0627 in 152,248 control chromosomes in the GnomAD database, including 357 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 0.063 (357 hom., cov: 33)
• Consequence: ENSG00000287923 ENST00000754737.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 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.415+25354C>T		intron	N/A
	ENSG00000287923	ENST00000754749.1		n.361+25354C>T		intron	N/A
	ENSG00000287923	ENST00000754750.1		n.733+25354C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0627 AC: 9540 AN: 152130 Hom.: 359 Cov.: 33

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0689

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0783

Gnomad FIN AF: 0.0511

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0673

Gnomad OTH AF: 0.0780

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

GnomAD4 genome AF: 0.0627 AC: 9539 AN: 152248 Hom.: 357 Cov.: 33 AF XY: 0.0622 AC XY: 4632 AN XY: 74448

African (AFR) AF: 0.0426 AC: 1770 AN: 41554

American (AMR) AF: 0.0687 AC: 1050 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0847 AC: 294 AN: 3470

East Asian (EAS) AF: 0.134 AC: 690 AN: 5168

South Asian (SAS) AF: 0.0779 AC: 376 AN: 4824

European-Finnish (FIN) AF: 0.0511 AC: 542 AN: 10612

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0673 AC: 4576 AN: 68018

Other (OTH) AF: 0.0781 AC: 165 AN: 2112

Alfa AF: 0.0678 Hom.: 689

Bravo AF: 0.0645

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.59
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs16968122; hg19: chr13-106717503;