chr2-17867386-C-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907737	XR_007086226.1	n.*206G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;