chr18-73655487-G-A

Variant names:

• chr18-73655487-G-A
• rs4892122
• ENST00000715567.1:n.65-1755C>T

Variant summary

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

The ENST00000715567.1(ENSG00000289131):​n.65-1755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,128 control chromosomes in the GnomAD database, including 36,746 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 0.69 (36746 hom., cov: 33)
• Consequence: ENSG00000289131 ENST00000715567.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 2 publications found

Genes affected

ENSG00000289131 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715567.1. 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
	ENSG00000289131	ENST00000715567.1		n.65-1755C>T		intron	N/A
	ENSG00000289131	ENST00000715568.1		n.63-84C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105584 AN: 152010 Hom.: 36725 Cov.: 33

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.695 AC: 105658 AN: 152128 Hom.: 36746 Cov.: 33 AF XY: 0.697 AC XY: 51854 AN XY: 74366

African (AFR) AF: 0.695 AC: 28857 AN: 41526

American (AMR) AF: 0.753 AC: 11503 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2459 AN: 3470

East Asian (EAS) AF: 0.796 AC: 4106 AN: 5156

South Asian (SAS) AF: 0.630 AC: 3040 AN: 4822

European-Finnish (FIN) AF: 0.747 AC: 7904 AN: 10576

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45622 AN: 67978

Other (OTH) AF: 0.685 AC: 1447 AN: 2112

Alfa AF: 0.685 Hom.: 4844

Bravo AF: 0.698

Asia WGS AF: 0.721 AC: 2510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.61
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs4892122; hg19: chr18-71322722;