18-55863647-A-T

Variant names:

• chr18-55863647-A-T
• rs9675567
• ENST00000729561.1:n.786-1937A>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000729561.1(ENSG00000267284):​n.786-1937A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,990 control chromosomes in the GnomAD database, including 29,560 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 0.62 (29560 hom., cov: 32)
• Consequence: ENSG00000267284 ENST00000729561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.44
• Publications: 0 publications found

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729561.1. 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	ENST00000729561.1		n.786-1937A>T		intron	N/A
	ENSG00000295387	ENST00000729712.1		n.168+169T>A		intron	N/A
	ENSG00000295387	ENST00000729713.1		n.112+2303T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93909 AN: 151872 Hom.: 29549 Cov.: 32

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.618 AC: 93957 AN: 151990 Hom.: 29560 Cov.: 32 AF XY: 0.627 AC XY: 46572 AN XY: 74286

African (AFR) AF: 0.570 AC: 23627 AN: 41436

American (AMR) AF: 0.613 AC: 9373 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2089 AN: 3472

East Asian (EAS) AF: 0.985 AC: 5078 AN: 5154

South Asian (SAS) AF: 0.777 AC: 3742 AN: 4814

European-Finnish (FIN) AF: 0.708 AC: 7488 AN: 10570

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40394 AN: 67952

Other (OTH) AF: 0.628 AC: 1325 AN: 2110

Alfa AF: 0.598 Hom.: 3380

Bravo AF: 0.612

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	19
DANN	Benign	0.86
PhyloP100		2.4

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: rs9675567;

hg19: chr18-53530878;