18-27787293-T-C

Variant names:

• chr18-27787293-T-C
• rs7234985
• ENST00000663298.1:n.188+1285T>C

Variant summary

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

The ENST00000663298.1(ENSG00000286426):​n.188+1285T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,898 control chromosomes in the GnomAD database, including 6,230 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 0.28 (6230 hom., cov: 32)
• Consequence: ENSG00000286426 ENST00000663298.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 1 publications found

Genes affected

ENSG00000286426 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663298.1. 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
	ENSG00000286426	ENST00000663298.1		n.188+1285T>C		intron	N/A
	ENSG00000297707	ENST00000750368.1		n.697+781A>G		intron	N/A
	ENSG00000297707	ENST00000750369.1		n.301+781A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41962 AN: 151778 Hom.: 6203 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.277 AC: 42031 AN: 151898 Hom.: 6230 Cov.: 32 AF XY: 0.275 AC XY: 20384 AN XY: 74220

African (AFR) AF: 0.354 AC: 14645 AN: 41422

American (AMR) AF: 0.257 AC: 3924 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 999 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1823 AN: 5130

South Asian (SAS) AF: 0.308 AC: 1483 AN: 4816

European-Finnish (FIN) AF: 0.181 AC: 1913 AN: 10544

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16393 AN: 67928

Other (OTH) AF: 0.292 AC: 617 AN: 2114

Alfa AF: 0.249 Hom.: 1307

Bravo AF: 0.285

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.29
PhyloP100		0.022

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: rs7234985;

hg19: chr18-25367257;