rs8099455

Variant names:

• chr18-61593940-G-A
• rs8099455
• ENST00000587754.1:n.501-1317C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-61593940-G-A
• chr18-61593940-G-T

Variant summary

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

The ENST00000587754.1(ENSG00000267175):​n.501-1317C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,984 control chromosomes in the GnomAD database, including 4,153 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 0.23 (4153 hom., cov: 31)
• Consequence: ENSG00000267175 ENST00000587754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 5 publications found

Genes affected

ENSG00000267175 (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 (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000587754.1. 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
	ENSG00000267175	ENST00000587754.1	TSL:5	n.501-1317C>T		intron	N/A
	ENSG00000267175	ENST00000590199.6	TSL:3	n.622-1317C>T		intron	N/A
	ENSG00000267175	ENST00000590968.1	TSL:2	n.318-1317C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34672 AN: 151868 Hom.: 4148 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.228 AC: 34714 AN: 151984 Hom.: 4153 Cov.: 31 AF XY: 0.228 AC XY: 16934 AN XY: 74306

African (AFR) AF: 0.277 AC: 11488 AN: 41440

American (AMR) AF: 0.275 AC: 4203 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3466

East Asian (EAS) AF: 0.378 AC: 1947 AN: 5148

South Asian (SAS) AF: 0.203 AC: 975 AN: 4808

European-Finnish (FIN) AF: 0.141 AC: 1491 AN: 10592

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12836 AN: 67952

Other (OTH) AF: 0.248 AC: 524 AN: 2110

Alfa AF: 0.210 Hom.: 6020

Bravo AF: 0.244

Asia WGS AF: 0.299 AC: 1043 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	2.1
DANN	Benign	0.88
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs8099455; hg19: chr18-59261173;