rs17519016

Variant names:

• chr18-53663720-T-A
• rs17519016
• XR_007066375.1:n.66+79665A>T

Variant summary

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

The XR_007066375.1(LOC124904304):​n.66+79665A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,090 control chromosomes in the GnomAD database, including 1,738 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 0.13 (1738 hom., cov: 33)
• Consequence: LOC124904304 XR_007066375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 1 publications found

Genes affected

LOC124904304 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19838 AN: 151972 Hom.: 1739 Cov.: 33

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.130 AC: 19837 AN: 152090 Hom.: 1738 Cov.: 33 AF XY: 0.132 AC XY: 9819 AN XY: 74334

African (AFR) AF: 0.0376 AC: 1563 AN: 41540

American (AMR) AF: 0.0874 AC: 1332 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3470

East Asian (EAS) AF: 0.0259 AC: 134 AN: 5176

South Asian (SAS) AF: 0.229 AC: 1103 AN: 4814

European-Finnish (FIN) AF: 0.239 AC: 2529 AN: 10596

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12297 AN: 67936

Other (OTH) AF: 0.126 AC: 266 AN: 2114

Alfa AF: 0.157 Hom.: 249

Bravo AF: 0.112

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.65
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs17519016; hg19: chr18-51190090;