17-45585159-T-G

Variant names:

• chr17-45585159-T-G
• rs1724427
• ENST00000807355.1:n.525A>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000807355.1(ENSG00000291175):​n.525A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.34 (2008 hom., cov: 35)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000291175 ENST00000807355.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.21
• Publications: 2 publications found

Genes affected

ENSG00000291175 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807355.1. 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
	ENSG00000291175	ENST00000807355.1		n.525A>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000285668	ENST00000807769.1		n.1334A>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000291175	ENST00000717223.1		n.560+543A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 35820 AN: 104732 Hom.: 2010 Cov.: 35

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.0801

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.477

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.400

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.342 AC: 35811 AN: 104816 Hom.: 2008 Cov.: 35 AF XY: 0.330 AC XY: 16714 AN XY: 50704

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.138 AC: 3705 AN: 26762

American (AMR) AF: 0.360 AC: 3836 AN: 10670

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1219 AN: 2538

East Asian (EAS) AF: 0.0797 AC: 245 AN: 3074

South Asian (SAS) AF: 0.421 AC: 1448 AN: 3436

European-Finnish (FIN) AF: 0.289 AC: 1904 AN: 6588

Middle Eastern (MID) AF: 0.471 AC: 99 AN: 210

European-Non Finnish (NFE) AF: 0.454 AC: 22451 AN: 49414

Other (OTH) AF: 0.400 AC: 569 AN: 1424

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.256 Hom.: 1062

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.34
PhyloP100		3.2

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: rs1724427;

hg19: chr17-43662525;