chr18-13999381-G-A

Variant names:

• chr18-13999381-G-A
• rs8093228
• ENST00000725536.1:n.82+957G>A

Variant summary

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

The ENST00000725536.1(ENSG00000294733):​n.82+957G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,016 control chromosomes in the GnomAD database, including 8,235 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 0.32 (8235 hom., cov: 32)
• Consequence: ENSG00000294733 ENST00000725536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 6 publications found

Genes affected

ENSG00000294733 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725536.1. 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
	ENSG00000294733	ENST00000725536.1		n.82+957G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48392 AN: 151898 Hom.: 8223 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.319 AC: 48442 AN: 152016 Hom.: 8235 Cov.: 32 AF XY: 0.315 AC XY: 23386 AN XY: 74326

African (AFR) AF: 0.434 AC: 17981 AN: 41436

American (AMR) AF: 0.284 AC: 4339 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3466

East Asian (EAS) AF: 0.129 AC: 667 AN: 5174

South Asian (SAS) AF: 0.271 AC: 1305 AN: 4814

European-Finnish (FIN) AF: 0.246 AC: 2593 AN: 10560

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19439 AN: 67990

Other (OTH) AF: 0.312 AC: 657 AN: 2104

Alfa AF: 0.295 Hom.: 3459

Bravo AF: 0.323

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.73
PhyloP100		-0.037

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: rs8093228;

hg19: chr18-13999380;