ENST00000654435.2:n.477C>T

Variant names:

• chr8-19245054-G-A
• rs11787341
• ENST00000654435.2:n.477C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654435.2(ENSG00000253557):​n.477C>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 0.0723 in 152,142 control chromosomes in the GnomAD database, including 545 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 0.072 (545 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000253557 ENST00000654435.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 4 publications found

Genes affected

ENSG00000253557 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654435.2. 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
	LOC100128993	NR_038919.1		n.375+94C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253557	ENST00000654435.2		n.477C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000253557	ENST00000517949.5	TSL:3	n.342+94C>T		intron	N/A
	ENSG00000253557	ENST00000520920.5	TSL:4	n.281+1655C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10977 AN: 152024 Hom.: 541 Cov.: 33

Gnomad AFR AF: 0.0598

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0862

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0703

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 578 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 266

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) AF: 0.00 AC: 0 AN: 570

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 8

GnomAD4 genome AF: 0.0723 AC: 10994 AN: 152142 Hom.: 545 Cov.: 33 AF XY: 0.0765 AC XY: 5686 AN XY: 74370

African (AFR) AF: 0.0597 AC: 2479 AN: 41496

American (AMR) AF: 0.169 AC: 2575 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3472

East Asian (EAS) AF: 0.125 AC: 646 AN: 5164

South Asian (SAS) AF: 0.0860 AC: 415 AN: 4824

European-Finnish (FIN) AF: 0.0726 AC: 769 AN: 10586

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0548 AC: 3729 AN: 68012

Other (OTH) AF: 0.0691 AC: 146 AN: 2112

Alfa AF: 0.0695 Hom.: 242

Bravo AF: 0.0777

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.78
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11787341; hg19: chr8-19102564;