18-28824808-C-T

Variant names:

• chr18-28824808-C-T
• rs1518589
• ENST00000603176.1:n.19G>A

Variant summary

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

The ENST00000603176.1(ENSG00000271238):​n.19G>A 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 0.375 in 152,000 control chromosomes in the GnomAD database, including 12,760 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 0.37 (12757 hom., cov: 31)
  • Exomes 𝑓: 0.50 (3 hom.)
• Consequence: ENSG00000271238 ENST00000603176.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.921
• Publications: 0 publications found

Genes affected

ENSG00000271238 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000603176.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000271238	ENST00000603176.1	TSL:6	n.19G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56978 AN: 151864 Hom.: 12756 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.442

GnomAD4 exome AF: 0.500 AC: 9 AN: 18 Hom.: 3 Cov.: 0 AF XY: 0.667 AC XY: 8 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 9 AN: 18

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.375 AC: 56990 AN: 151982 Hom.: 12757 Cov.: 31 AF XY: 0.373 AC XY: 27737 AN XY: 74288

African (AFR) AF: 0.126 AC: 5217 AN: 41498

American (AMR) AF: 0.406 AC: 6190 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2015 AN: 3470

East Asian (EAS) AF: 0.239 AC: 1229 AN: 5150

South Asian (SAS) AF: 0.384 AC: 1847 AN: 4816

European-Finnish (FIN) AF: 0.468 AC: 4935 AN: 10546

Middle Eastern (MID) AF: 0.514 AC: 149 AN: 290

European-Non Finnish (NFE) AF: 0.501 AC: 34013 AN: 67934

Other (OTH) AF: 0.445 AC: 938 AN: 2106

Alfa AF: 0.463 Hom.: 9143

Bravo AF: 0.364

Asia WGS AF: 0.327 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	8.1
DANN	Benign	0.13
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs1518589; hg19: chr18-26404772;