rs784237

Variant names:

• chr18-55748883-T-A
• rs784237
• ENST00000587346.1:n.140-12420T>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000587346.1. 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
	ENSG00000267284	ENST00000587346.1	TSL:4	n.140-12420T>A		intron	N/A
	ENSG00000267284	ENST00000589662.1	TSL:5	n.217+27349T>A		intron	N/A
	ENSG00000267284	ENST00000592936.1	TSL:4	n.473-10157T>A		intron	N/A

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

African (AFR) AF: 0.881 AC: 36611 AN: 41544

American (AMR) AF: 0.910 AC: 13922 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2759 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5171 AN: 5182

South Asian (SAS) AF: 0.789 AC: 3801 AN: 4820

European-Finnish (FIN) AF: 0.870 AC: 9215 AN: 10594

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56600 AN: 68010

Other (OTH) AF: 0.879 AC: 1856 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.27
DANN	Benign	0.53
PhyloP100		-0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs784237;

hg19: chr18-53416114;