rs3025343

Positions:

• chr9-133613233-G-A

Variant summary

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

The ENST00000564021.1(ENSG00000261018):​n.555C>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 0.0694 in 152,234 control chromosomes in the GnomAD database, including 504 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 0.069 (504 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000564021.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000564021.1	n.555C>T		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.0694 AC: 10558 AN: 152116 Hom.: 504 Cov.: 33

Gnomad AFR AF: 0.0215

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0715

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0272

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0779

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0694 AC: 10559 AN: 152234 Hom.: 504 Cov.: 33 AF XY: 0.0644 AC XY: 4796 AN XY: 74452

Gnomad4 AFR AF: 0.0215

Gnomad4 AMR AF: 0.0714

Gnomad4 ASJ AF: 0.0637

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0166

Gnomad4 FIN AF: 0.0272

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0766

Alfa AF: 0.0991 Hom.: 1108

Bravo AF: 0.0684

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.75
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3025343; hg19: chr9-136478355;