rs2184898

Variant names:

• chr10-117658593-G-A
• rs2184898
• ENST00000806653.1:n.93-16908G>A

Variant summary

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

The ENST00000806653.1(ENSG00000304858):​n.93-16908G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,888 control chromosomes in the GnomAD database, including 8,284 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 0.32 (8284 hom., cov: 32)
• Consequence: ENSG00000304858 ENST00000806653.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 14 publications found

Genes affected

ENSG00000304858 (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 (NFE) allele frequency at 95% confidence interval = 0.392 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
ENSG00000304858	ENST00000806653.1	n.93-16908G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47953 AN: 151770 Hom.: 8283 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.316 AC: 47960 AN: 151888 Hom.: 8284 Cov.: 32 AF XY: 0.312 AC XY: 23126 AN XY: 74226

African (AFR) AF: 0.204 AC: 8465 AN: 41416

American (AMR) AF: 0.280 AC: 4279 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3466

East Asian (EAS) AF: 0.167 AC: 865 AN: 5176

South Asian (SAS) AF: 0.251 AC: 1206 AN: 4810

European-Finnish (FIN) AF: 0.382 AC: 4016 AN: 10508

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26903 AN: 67930

Other (OTH) AF: 0.293 AC: 617 AN: 2108

Alfa AF: 0.368 Hom.: 46976

Bravo AF: 0.304

Asia WGS AF: 0.216 AC: 749 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	0.25
DANN	Benign	0.63
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2184898; hg19: chr10-119418104;