ENST00000840058.1:n.466T>C

Variant names:

• chr9-42295738-T-C
• rs3007456
• ENST00000840058.1:n.466T>C

Variant summary

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

The ENST00000840058.1(ENSG00000275649):​n.466T>C 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 0.818 in 133,392 control chromosomes in the GnomAD database, including 48,192 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 0.82 (48192 hom., cov: 23)
• Consequence: ENSG00000275649 ENST00000840058.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 1 publications found

Genes affected

ENSG00000275649 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.88 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
ENSG00000275649	ENST00000840058.1	n.466T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000275649	ENST00000614030.1	n.27-28168T>C		intron_variant	Intron 1 of 3	5
ENSG00000275649	ENST00000840056.1	n.400-28168T>C		intron_variant	Intron 1 of 3
ENSG00000275649	ENST00000840057.1	n.364-28168T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.818 AC: 109032 AN: 133278 Hom.: 48157 Cov.: 23

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.881

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.823

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.818 AC: 109116 AN: 133392 Hom.: 48192 Cov.: 23 AF XY: 0.820 AC XY: 53040 AN XY: 64716

African (AFR) AF: 0.633 AC: 21627 AN: 34150

American (AMR) AF: 0.880 AC: 11665 AN: 13258

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2596 AN: 3158

East Asian (EAS) AF: 0.827 AC: 3595 AN: 4346

South Asian (SAS) AF: 0.872 AC: 3589 AN: 4114

European-Finnish (FIN) AF: 0.912 AC: 8407 AN: 9214

Middle Eastern (MID) AF: 0.883 AC: 249 AN: 282

European-Non Finnish (NFE) AF: 0.886 AC: 55100 AN: 62200

Other (OTH) AF: 0.820 AC: 1487 AN: 1814

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.28
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs3007456; hg19: chr9-43518651;