rs17083844

Variant names:

• chr18-71175007-G-A
• rs17083844
• ENST00000658819.1:n.192-22931G>A

Variant summary

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

The ENST00000658819.1(ENSG00000287693):​n.192-22931G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0698 in 152,096 control chromosomes in the GnomAD database, including 590 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 0.070 (590 hom., cov: 32)
• Consequence: ENSG00000287693 ENST00000658819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 8 publications found

Genes affected

ENSG00000287693 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 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
ENSG00000287693	ENST00000658819.1	n.192-22931G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0696 AC: 10584 AN: 151978 Hom.: 583 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0253

Gnomad EAS AF: 0.0610

Gnomad SAS AF: 0.0545

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0317

Gnomad OTH AF: 0.0725

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

GnomAD4 genome AF: 0.0698 AC: 10620 AN: 152096 Hom.: 590 Cov.: 32 AF XY: 0.0697 AC XY: 5181 AN XY: 74362

African (AFR) AF: 0.143 AC: 5927 AN: 41488

American (AMR) AF: 0.0935 AC: 1427 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0253 AC: 88 AN: 3472

East Asian (EAS) AF: 0.0613 AC: 317 AN: 5172

South Asian (SAS) AF: 0.0545 AC: 263 AN: 4826

European-Finnish (FIN) AF: 0.0231 AC: 244 AN: 10582

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0317 AC: 2157 AN: 67990

Other (OTH) AF: 0.0726 AC: 153 AN: 2106

Alfa AF: 0.0470 Hom.: 729

Bravo AF: 0.0794

Asia WGS AF: 0.0920 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.67
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs17083844; hg19: chr18-68842243;