17-409857-G-A

Position:

• chr17-409857-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000599026.1(ENSG00000241525):​n.175C>T 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 0.347 in 153,352 control chromosomes in the GnomAD database, including 10,823 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 0.35 (10757 hom., cov: 31)
  • Exomes 𝑓: 0.26 (66 hom.)
• Consequence: ENSG00000241525 ENST00000599026.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

Genes affected

ENSG00000241525 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371430	NR_136407.1	n.330+3272C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000241525	ENST00000599026.1	n.175C>T		non_coding_transcript_exon_variant	1/2	5
ENSG00000241525	ENST00000466740.2	n.330+3272C>T		intron_variant		3
ENSG00000241525	ENST00000629249.1	n.255+3272C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52698 AN: 151714 Hom.: 10730 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.318

GnomAD4 exome AF: 0.261 AC: 397 AN: 1520 Hom.: 66 Cov.: 0 AF XY: 0.267 AC XY: 248 AN XY: 928

Gnomad4 AFR exome AF: 0.531

Gnomad4 AMR exome AF: 0.100

Gnomad4 ASJ exome AF: 0.214

Gnomad4 EAS exome AF: 0.375

Gnomad4 SAS exome AF: 0.347

Gnomad4 FIN exome AF: 0.119

Gnomad4 NFE exome AF: 0.186

Gnomad4 OTH exome AF: 0.284

GnomAD4 genome AF: 0.348 AC: 52783 AN: 151832 Hom.: 10757 Cov.: 31 AF XY: 0.345 AC XY: 25570 AN XY: 74218

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.316

Alfa AF: 0.248 Hom.: 6772

Bravo AF: 0.361

Asia WGS AF: 0.331 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11150882; hg19: chr17-259648;