18-21906764-T-C

Variant names:

• chr18-21906764-T-C
• rs7239116
• ENST00000778525.1:n.260-8483T>C

Variant summary

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

The ENST00000778525.1(ENSG00000301367):​n.260-8483T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,014 control chromosomes in the GnomAD database, including 14,091 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 0.42 (14091 hom., cov: 32)
• Consequence: ENSG00000301367 ENST00000778525.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680
• Publications: 4 publications found

Genes affected

ENSG00000301367 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778525.1. 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
	ENSG00000301367	ENST00000778525.1		n.260-8483T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63418 AN: 151896 Hom.: 14068 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.418 AC: 63501 AN: 152014 Hom.: 14091 Cov.: 32 AF XY: 0.422 AC XY: 31335 AN XY: 74308

African (AFR) AF: 0.557 AC: 23082 AN: 41428

American (AMR) AF: 0.507 AC: 7739 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1296 AN: 3466

East Asian (EAS) AF: 0.416 AC: 2148 AN: 5166

South Asian (SAS) AF: 0.450 AC: 2173 AN: 4828

European-Finnish (FIN) AF: 0.366 AC: 3866 AN: 10556

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21893 AN: 67992

Other (OTH) AF: 0.424 AC: 894 AN: 2108

Alfa AF: 0.362 Hom.: 12711

Bravo AF: 0.432

Asia WGS AF: 0.506 AC: 1760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.71
DANN	Benign	0.69
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs7239116; hg19: chr18-19486725;