rs4892122

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372190	XR_007066468.1	n.64-84C>T		intron_variant	Intron 1 of 6
LOC105372190	XR_007066469.1	n.171-84C>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289131	ENST00000715567.1	n.65-1755C>T		intron_variant	Intron 1 of 2
ENSG00000289131	ENST00000715568.1	n.63-84C>T		intron_variant	Intron 1 of 3

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 v4.3

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;