18-68290555-C-T

Variant names:

• chr18-68290555-C-T
• rs543152
• ENST00000661028.2:n.644+37408G>A

Variant summary

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

The ENST00000661028.2(ENSG00000287907):​n.644+37408G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,100 control chromosomes in the GnomAD database, including 2,512 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 0.17 (2512 hom., cov: 32)
• Consequence: ENSG00000287907 ENST00000661028.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 2 publications found

Genes affected

ENSG00000287907 (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 (NFE) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287907	ENST00000661028.2	n.644+37408G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26070 AN: 151982 Hom.: 2508 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.171 AC: 26079 AN: 152100 Hom.: 2512 Cov.: 32 AF XY: 0.169 AC XY: 12588 AN XY: 74336

African (AFR) AF: 0.101 AC: 4200 AN: 41516

American (AMR) AF: 0.201 AC: 3064 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3466

East Asian (EAS) AF: 0.0650 AC: 336 AN: 5170

South Asian (SAS) AF: 0.126 AC: 605 AN: 4814

European-Finnish (FIN) AF: 0.171 AC: 1806 AN: 10558

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14876 AN: 67982

Other (OTH) AF: 0.182 AC: 384 AN: 2112

Alfa AF: 0.200 Hom.: 1719

Bravo AF: 0.170

Asia WGS AF: 0.0930 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.56
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs543152; hg19: chr18-65957792;