18-21113636-G-T

Variant names:

• chr18-21113636-G-T
• rs8089974
• ENST00000833849.1:n.1048+718G>T

Variant summary

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

The ENST00000833849.1(ENSG00000308413):​n.1048+718G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 151,920 control chromosomes in the GnomAD database, including 52,999 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 0.80 (52999 hom., cov: 30)
• Consequence: ENSG00000308413 ENST00000833849.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 5 publications found

Genes affected

ENSG00000308413 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000833849.1. 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
	ENSG00000308413	ENST00000833849.1		n.1048+718G>T		intron	N/A
	ENSG00000308413	ENST00000833850.1		n.975+718G>T		intron	N/A
	ENSG00000308413	ENST00000833851.1		n.731+718G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122096 AN: 151804 Hom.: 53010 Cov.: 30

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.804 AC: 122115 AN: 151920 Hom.: 52999 Cov.: 30 AF XY: 0.807 AC XY: 59968 AN XY: 74270

African (AFR) AF: 0.444 AC: 18340 AN: 41298

American (AMR) AF: 0.807 AC: 12336 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3218 AN: 3472

East Asian (EAS) AF: 0.912 AC: 4702 AN: 5158

South Asian (SAS) AF: 0.965 AC: 4652 AN: 4820

European-Finnish (FIN) AF: 0.977 AC: 10346 AN: 10588

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.965 AC: 65604 AN: 67992

Other (OTH) AF: 0.835 AC: 1759 AN: 2106

Alfa AF: 0.856 Hom.: 7634

Bravo AF: 0.773

Asia WGS AF: 0.895 AC: 3108 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.37
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs8089974; hg19: chr18-18693597;