chr18-74211282-C-A

Variant names:

• chr18-74211282-C-A
• rs9951925
• ENST00000562795.1:n.*109G>T

Variant summary

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

The ENST00000562795.1(ENSG00000260569):​n.*109G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 152,072 control chromosomes in the GnomAD database, including 20,543 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 0.52 (20543 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000260569 ENST00000562795.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 7 publications found

Genes affected

ENSG00000260569 (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 = 0.569 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
ENSG00000260569	ENST00000562795.1	n.*109G>T		downstream_gene_variant		6
ENSG00000260569	ENST00000580403.1	n.*109G>T		downstream_gene_variant		2
ENSG00000260569	ENST00000775031.1	n.*104G>T		downstream_gene_variant
ENSG00000260569	ENST00000775032.1	n.*104G>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78505 AN: 151954 Hom.: 20510 Cov.: 33

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.525

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.517 AC: 78594 AN: 152072 Hom.: 20543 Cov.: 33 AF XY: 0.512 AC XY: 38039 AN XY: 74334

African (AFR) AF: 0.576 AC: 23878 AN: 41486

American (AMR) AF: 0.524 AC: 8000 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1540 AN: 3472

East Asian (EAS) AF: 0.281 AC: 1452 AN: 5176

South Asian (SAS) AF: 0.450 AC: 2170 AN: 4818

European-Finnish (FIN) AF: 0.449 AC: 4738 AN: 10548

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35069 AN: 67978

Other (OTH) AF: 0.525 AC: 1108 AN: 2112

Alfa AF: 0.513 Hom.: 16439

Bravo AF: 0.529

Asia WGS AF: 0.362 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.39
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs9951925; hg19: chr18-71878517;