18-2292492-C-T

Variant names:

• chr18-2292492-C-T
• rs627202
• ENST00000639316.2:n.354+42578G>A

Variant summary

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

The ENST00000746279.1(ENSG00000263745):​n.185+42578G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 151,294 control chromosomes in the GnomAD database, including 23,065 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 0.55 (23065 hom., cov: 30)
• Consequence: ENSG00000263745 ENST00000746279.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 2 publications found

Genes affected

ENSG00000263745 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746279.1. 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
	ENSG00000263745	ENST00000639316.2	TSL:5	n.354+42578G>A		intron	N/A
	ENSG00000263745	ENST00000746279.1		n.185+42578G>A		intron	N/A
	ENSG00000263745	ENST00000746280.1		n.96+34580G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83272 AN: 151178 Hom.: 23028 Cov.: 30

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.551 AC: 83363 AN: 151294 Hom.: 23065 Cov.: 30 AF XY: 0.546 AC XY: 40386 AN XY: 73906

African (AFR) AF: 0.575 AC: 23719 AN: 41266

American (AMR) AF: 0.552 AC: 8398 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1975 AN: 3464

East Asian (EAS) AF: 0.699 AC: 3572 AN: 5112

South Asian (SAS) AF: 0.551 AC: 2645 AN: 4802

European-Finnish (FIN) AF: 0.443 AC: 4592 AN: 10372

Middle Eastern (MID) AF: 0.486 AC: 140 AN: 288

European-Non Finnish (NFE) AF: 0.542 AC: 36702 AN: 67774

Other (OTH) AF: 0.565 AC: 1186 AN: 2098

Alfa AF: 0.549 Hom.: 71444

Bravo AF: 0.561

Asia WGS AF: 0.623 AC: 2163 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.36
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs627202; hg19: chr18-2292491;