18-42098864-T-G

Variant names:

• chr18-42098864-T-G
• rs627636
• ENST00000721786.1:n.250-9097A>C

Variant summary

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

The ENST00000721786.1(ENSG00000287007):​n.250-9097A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,850 control chromosomes in the GnomAD database, including 20,899 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 0.50 (20899 hom., cov: 32)
• Consequence: ENSG00000287007 ENST00000721786.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907
• Publications: 6 publications found

Genes affected

ENSG00000287007 (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 = 0.724 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000721786.1. 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
	ENSG00000287007	ENST00000721786.1		n.250-9097A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76120 AN: 151732 Hom.: 20846 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.502 AC: 76237 AN: 151850 Hom.: 20899 Cov.: 32 AF XY: 0.504 AC XY: 37425 AN XY: 74186

African (AFR) AF: 0.731 AC: 30274 AN: 41414

American (AMR) AF: 0.533 AC: 8123 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1179 AN: 3466

East Asian (EAS) AF: 0.627 AC: 3241 AN: 5166

South Asian (SAS) AF: 0.511 AC: 2458 AN: 4812

European-Finnish (FIN) AF: 0.379 AC: 3981 AN: 10516

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25483 AN: 67918

Other (OTH) AF: 0.465 AC: 984 AN: 2114

Alfa AF: 0.396 Hom.: 10702

Bravo AF: 0.523

Asia WGS AF: 0.601 AC: 2094 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	0.30
DANN	Benign	0.74
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs627636; hg19: chr18-39678828;