rs8088001

Variant names:

• chr18-287705-T-G
• rs8088001

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.137 in 152,108 control chromosomes in the GnomAD database, including 2,121 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 0.14 (2121 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 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

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20791 AN: 151990 Hom.: 2118 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0786

Gnomad ASJ AF: 0.0900

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.137 AC: 20825 AN: 152108 Hom.: 2121 Cov.: 32 AF XY: 0.140 AC XY: 10395 AN XY: 74372

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.0785

Gnomad4 ASJ AF: 0.0900

Gnomad4 EAS AF: 0.0413

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0757

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0888 Hom.: 1080

Bravo AF: 0.139

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8088001; hg19: chr18-287705;