rs17526895

Variant names:

• chr2-118058382-A-G
• rs17526895
• ENST00000747900.1:n.958A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000747900.1(ENSG00000235066):​n.958A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0517 in 152,296 control chromosomes in the GnomAD database, including 273 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 0.052 (273 hom., cov: 33)
• Consequence: ENSG00000235066 ENST00000747900.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29
• Publications: 9 publications found

Genes affected

ENSG00000235066 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747900.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000235066	ENST00000747900.1		n.958A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000297418	ENST00000747789.1		n.232-12689T>C		intron	N/A
	ENSG00000297418	ENST00000747790.1		n.105-28063T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0518 AC: 7881 AN: 152178 Hom.: 274 Cov.: 33

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.0525

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0530

Gnomad FIN AF: 0.0610

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0517 AC: 7874 AN: 152296 Hom.: 273 Cov.: 33 AF XY: 0.0500 AC XY: 3722 AN XY: 74468

African (AFR) AF: 0.0128 AC: 532 AN: 41576

American (AMR) AF: 0.0352 AC: 538 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0525 AC: 182 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0529 AC: 255 AN: 4824

European-Finnish (FIN) AF: 0.0610 AC: 647 AN: 10602

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0815 AC: 5542 AN: 68020

Other (OTH) AF: 0.0473 AC: 100 AN: 2112

Alfa AF: 0.0685 Hom.: 869

Bravo AF: 0.0477

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	17
DANN	Benign	0.65
PhyloP100		2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17526895;

hg19: chr2-118815958;