ENST00000754737.1:n.129-54476A>C

Variant names:

• chr13-106145270-T-G
• rs17182039
• ENST00000754737.1:n.129-54476A>C

Variant summary

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

The ENST00000754737.1(ENSG00000287923):​n.129-54476A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0979 in 152,264 control chromosomes in the GnomAD database, including 939 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 0.098 (939 hom., cov: 32)
• Consequence: ENSG00000287923 ENST00000754737.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402
• 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 (EAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287923	ENST00000754737.1	n.129-54476A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0978 AC: 14874 AN: 152146 Hom.: 936 Cov.: 32

Gnomad AFR AF: 0.0842

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0979 AC: 14902 AN: 152264 Hom.: 939 Cov.: 32 AF XY: 0.0993 AC XY: 7391 AN XY: 74456

African (AFR) AF: 0.0847 AC: 3520 AN: 41558

American (AMR) AF: 0.183 AC: 2802 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 371 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1102 AN: 5174

South Asian (SAS) AF: 0.162 AC: 782 AN: 4828

European-Finnish (FIN) AF: 0.0506 AC: 538 AN: 10622

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0805 AC: 5472 AN: 68002

Other (OTH) AF: 0.106 AC: 223 AN: 2112

Alfa AF: 0.0616 Hom.: 115

Bravo AF: 0.112

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.45
DANN	Benign	0.64
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs17182039; hg19: chr13-106797619;