chr17-45585159-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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291175	ENST00000807355.1	n.525A>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000285668	ENST00000807769.1	n.1334A>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000291175	ENST00000717223.1	n.560+543A>C		intron_variant	Intron 1 of 9

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 = 0.000000), 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 v4.3

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

Other links and lift over

dbSNP: rs1724427; hg19: chr17-43662525;