rs3025343

Variant names:

• chr9-133613233-G-A
• rs3025343
• ENST00000564021.1:n.555C>T

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000261018 ENST00000564021.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 55 publications found

Genes affected

ENSG00000261018 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261018	ENST00000564021.1	n.555C>T		non_coding_transcript_exon_variant	Exon 2 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 12

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0215 AC: 892 AN: 41536

American (AMR) AF: 0.0714 AC: 1091 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0166 AC: 80 AN: 4818

European-Finnish (FIN) AF: 0.0272 AC: 288 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7780 AN: 68010

Other (OTH) AF: 0.0766 AC: 162 AN: 2114

Alfa AF: 0.0956 Hom.: 2556

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
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs3025343; hg19: chr9-136478355;