18-50959597-A-G

Variant names:

• chr18-50959597-A-G
• rs606073
• ENST00000363882.1:n.-218T>C

Variant summary

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

The ENST00000363882.1(Y_RNA):​n.-218T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,928 control chromosomes in the GnomAD database, including 21,458 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 0.51 (21458 hom., cov: 31)
• Consequence: Y_RNA ENST00000363882.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 4 publications found

Genes affected

Y_RNA (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000363882.1. 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
	Y_RNA	ENST00000363882.1	TSL:6	n.-218T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77148 AN: 151810 Hom.: 21416 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.508 AC: 77251 AN: 151928 Hom.: 21458 Cov.: 31 AF XY: 0.506 AC XY: 37529 AN XY: 74232

African (AFR) AF: 0.750 AC: 31079 AN: 41432

American (AMR) AF: 0.449 AC: 6848 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1614 AN: 3468

East Asian (EAS) AF: 0.543 AC: 2797 AN: 5152

South Asian (SAS) AF: 0.325 AC: 1565 AN: 4816

European-Finnish (FIN) AF: 0.418 AC: 4408 AN: 10538

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27173 AN: 67938

Other (OTH) AF: 0.500 AC: 1056 AN: 2114

Alfa AF: 0.442 Hom.: 50040

Bravo AF: 0.530

Asia WGS AF: 0.457 AC: 1587 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.1
DANN	Benign	0.87
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs606073; hg19: chr18-48485967;