ENST00000812688.1:n.183+13853G>T

Variant names:

• chr5-152351716-G-T
• rs17113138
• ENST00000812688.1:n.183+13853G>T

Variant summary

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

The ENST00000812688.1(ENSG00000286749):​n.183+13853G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,052 control chromosomes in the GnomAD database, including 9,187 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 0.33 (9187 hom., cov: 32)
• Consequence: ENSG00000286749 ENST00000812688.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578
• Publications: 4 publications found

Genes affected

ENSG00000286749 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378237	XR_944433.2	n.197+13853G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286749	ENST00000812688.1	n.183+13853G>T		intron_variant	Intron 2 of 3
ENSG00000286749	ENST00000812689.1	n.172+13853G>T		intron_variant	Intron 2 of 4
ENSG00000286749	ENST00000812690.1	n.144+13853G>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50707 AN: 151936 Hom.: 9167 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.334 AC: 50770 AN: 152052 Hom.: 9187 Cov.: 32 AF XY: 0.333 AC XY: 24715 AN XY: 74320

African (AFR) AF: 0.480 AC: 19893 AN: 41466

American (AMR) AF: 0.349 AC: 5333 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3466

East Asian (EAS) AF: 0.186 AC: 959 AN: 5164

South Asian (SAS) AF: 0.351 AC: 1685 AN: 4806

European-Finnish (FIN) AF: 0.266 AC: 2809 AN: 10578

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17994 AN: 67974

Other (OTH) AF: 0.332 AC: 702 AN: 2116

Alfa AF: 0.294 Hom.: 19137

Bravo AF: 0.348

Asia WGS AF: 0.318 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	17
DANN	Benign	0.59
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs17113138; hg19: chr5-151731277;