rs17316177

Variant names:

• chr2-17867386-C-T
• rs17316177
• XR_007086226.1:n.*206G>A

Variant summary

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

The XR_007086226.1(LOC124907737):​n.*206G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0944 in 152,212 control chromosomes in the GnomAD database, including 881 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 0.094 (881 hom., cov: 32)
• Consequence: LOC124907737 XR_007086226.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582
• Publications: 5 publications found

Genes affected

LOC124907737 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0944 AC: 14363 AN: 152094 Hom.: 877 Cov.: 32

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0782

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0944 AC: 14367 AN: 152212 Hom.: 881 Cov.: 32 AF XY: 0.0944 AC XY: 7019 AN XY: 74390

African (AFR) AF: 0.0313 AC: 1302 AN: 41538

American (AMR) AF: 0.0807 AC: 1234 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 684 AN: 3464

East Asian (EAS) AF: 0.0110 AC: 57 AN: 5178

South Asian (SAS) AF: 0.192 AC: 926 AN: 4828

European-Finnish (FIN) AF: 0.0782 AC: 827 AN: 10582

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8906 AN: 68018

Other (OTH) AF: 0.103 AC: 218 AN: 2108

Alfa AF: 0.118 Hom.: 2266

Bravo AF: 0.0887

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.1
DANN	Benign	0.57
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs17316177; hg19: chr2-18048653;