ENST00000819110.1:n.239-11698A>G

Variant names:

• chr5-163593753-T-C
• rs172389
• ENST00000819110.1:n.239-11698A>G

Variant summary

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

The ENST00000819110.1(ENSG00000285590):​n.239-11698A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.037 in 152,282 control chromosomes in the GnomAD database, including 133 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 0.037 (133 hom., cov: 32)
• Consequence: ENSG00000285590 ENST00000819110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 0 publications found

Genes affected

ENSG00000285590 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.055 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
ENSG00000285590	ENST00000819110.1	n.239-11698A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0370 AC: 5634 AN: 152164 Hom.: 133 Cov.: 32

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0378

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0364

Gnomad FIN AF: 0.0391

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0370 AC: 5628 AN: 152282 Hom.: 133 Cov.: 32 AF XY: 0.0369 AC XY: 2749 AN XY: 74464

African (AFR) AF: 0.0107 AC: 443 AN: 41572

American (AMR) AF: 0.0378 AC: 578 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3472

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5186

South Asian (SAS) AF: 0.0362 AC: 174 AN: 4804

European-Finnish (FIN) AF: 0.0391 AC: 415 AN: 10612

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0564 AC: 3839 AN: 68016

Other (OTH) AF: 0.0321 AC: 68 AN: 2116

Alfa AF: 0.0452 Hom.: 38

Bravo AF: 0.0343

Asia WGS AF: 0.0130 AC: 44 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.4
DANN	Benign	0.79
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs172389; hg19: chr5-163020759;