rs17217119

Variant names:

• chr20-54126051-A-G
• rs17217119
• ENST00000792273.1:n.154+15537A>G

Variant summary

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

The ENST00000792273.1(ENSG00000286587):​n.154+15537A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 151,762 control chromosomes in the GnomAD database, including 3,246 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 0.19 (3246 hom., cov: 32)
• Consequence: ENSG00000286587 ENST00000792273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 22 publications found

Genes affected

ENSG00000286587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.301 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
ENSG00000286587	ENST00000792273.1	n.154+15537A>G		intron_variant	Intron 2 of 3
ENSG00000286587	ENST00000792274.1	n.144+15537A>G		intron_variant	Intron 2 of 6
ENSG00000286587	ENST00000792275.1	n.186+15537A>G		intron_variant	Intron 1 of 2
ENSG00000286587	ENST00000792276.1	n.125+2134A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29485 AN: 151644 Hom.: 3243 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.194 AC: 29502 AN: 151762 Hom.: 3246 Cov.: 32 AF XY: 0.197 AC XY: 14647 AN XY: 74176

African (AFR) AF: 0.110 AC: 4576 AN: 41442

American (AMR) AF: 0.308 AC: 4706 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 748 AN: 3468

East Asian (EAS) AF: 0.144 AC: 744 AN: 5180

South Asian (SAS) AF: 0.308 AC: 1484 AN: 4820

European-Finnish (FIN) AF: 0.232 AC: 2397 AN: 10334

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14084 AN: 67938

Other (OTH) AF: 0.213 AC: 449 AN: 2106

Alfa AF: 0.211 Hom.: 5975

Bravo AF: 0.196

Asia WGS AF: 0.205 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.61
DANN	Benign	0.39
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs17217119; hg19: chr20-52742590;