ENST00000687285.2:n.123+10139G>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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376872	XR_935606.3	n.87+4815G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288828	ENST00000687285.2	n.123+10139G>A		intron_variant	Intron 1 of 3
ENSG00000288828	ENST00000798369.1	n.85+10139G>A		intron_variant	Intron 1 of 4
ENSG00000288828	ENST00000798370.1	n.81+10139G>A		intron_variant	Intron 1 of 5

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 v4.3

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;