rs784237

Positions:

• chr18-55748883-T-A
• chr18-55748883-T-C
• chr18-55748883-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000587346.1(ENSG00000267284):​n.140-12420T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,238 control chromosomes in the GnomAD database, including 56,447 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 0.86 (56447 hom., cov: 33)
• Consequence: ENSG00000267284 ENST00000587346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372130	XR_007066382.1	n.329-36016T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267284	ENST00000587346.1	n.140-12420T>A		intron_variant		4
ENSG00000267284	ENST00000589662.1	n.217+27349T>A		intron_variant		5
ENSG00000267284	ENST00000592936.1	n.473-10157T>A		intron_variant		4
ENSG00000267284	ENST00000654829.1	n.157-36016T>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130907 AN: 152120 Hom.: 56395 Cov.: 33

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.861 AC: 131013 AN: 152238 Hom.: 56447 Cov.: 33 AF XY: 0.863 AC XY: 64203 AN XY: 74426

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.879

Alfa AF: 0.819 Hom.: 2498

Bravo AF: 0.869

Asia WGS AF: 0.909 AC: 3159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.27
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs784237; hg19: chr18-53416114;