chr18-70475178-G-A

Variant names:

• chr18-70475178-G-A
• rs8092443
• ENST00000687285.2:n.123+10139G>A

Variant summary

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

The ENST00000687285.2(ENSG00000288828):​n.123+10139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,138 control chromosomes in the GnomAD database, including 3,811 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 0.21 (3811 hom., cov: 32)
• Consequence: ENSG00000288828 ENST00000687285.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 10 publications found

Genes affected

ENSG00000288828 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687285.2. 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
	ENSG00000288828	ENST00000687285.2		n.123+10139G>A		intron	N/A
	ENSG00000288828	ENST00000798369.1		n.85+10139G>A		intron	N/A
	ENSG00000288828	ENST00000798370.1		n.81+10139G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31278 AN: 152020 Hom.: 3802 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.206 AC: 31310 AN: 152138 Hom.: 3811 Cov.: 32 AF XY: 0.202 AC XY: 15001 AN XY: 74380

African (AFR) AF: 0.348 AC: 14441 AN: 41484

American (AMR) AF: 0.132 AC: 2021 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3472

East Asian (EAS) AF: 0.103 AC: 535 AN: 5178

South Asian (SAS) AF: 0.204 AC: 983 AN: 4818

European-Finnish (FIN) AF: 0.135 AC: 1430 AN: 10592

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.161 AC: 10939 AN: 67996

Other (OTH) AF: 0.188 AC: 397 AN: 2110

Alfa AF: 0.177 Hom.: 6244

Bravo AF: 0.212

Asia WGS AF: 0.173 AC: 598 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.33
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs8092443; hg19: chr18-68142414;