ENST00000792518.1:n.924A>T

Variant names:

• chr5-172771902-T-A
• rs881150
• ENST00000792518.1:n.924A>T

Variant summary

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

The ENST00000792518.1(ENSG00000289170):​n.924A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,228 control chromosomes in the GnomAD database, including 4,178 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 0.23 (4178 hom., cov: 33)
• Consequence: ENSG00000289170 ENST00000792518.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 12 publications found

Genes affected

ENSG00000289170 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792518.1. 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
	ENSG00000289170	ENST00000792518.1		n.924A>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000253736	ENST00000792668.1		n.276T>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000253736	ENST00000523005.1	TSL:3	n.70-5590T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34997 AN: 152110 Hom.: 4178 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0532

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.230 AC: 34999 AN: 152228 Hom.: 4178 Cov.: 33 AF XY: 0.228 AC XY: 16965 AN XY: 74434

African (AFR) AF: 0.237 AC: 9839 AN: 41534

American (AMR) AF: 0.183 AC: 2799 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3472

East Asian (EAS) AF: 0.0533 AC: 276 AN: 5178

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4822

European-Finnish (FIN) AF: 0.258 AC: 2735 AN: 10612

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17174 AN: 68000

Other (OTH) AF: 0.186 AC: 392 AN: 2110

Alfa AF: 0.249 Hom.: 600

Bravo AF: 0.220

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.7
DANN	Benign	0.90
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs881150; hg19: chr5-172198905;