Genetic Variant ENSG00000275716:n.458T>A (chr6-100093311-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000612765.1(ENSG00000275716):n.458T>A variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ENSG00000275716
ENST00000612765.1 splice_region, non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0510

Publications

1 publications found

Variant links:

Genes affected

ENSG00000275716 (HGNC:):

ENSG00000275716 links:

MCHR2-AS1 (HGNC:48980): (MCHR2 antisense RNA 1)

MCHR2-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100420742		n.100093311A>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000275716	ENST00000612765.1 link	n.458T>A	splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 1	6
MCHR2-AS1	ENST00000661108.2 link	n.373-14198A>T	intron_variant	Intron 2 of 2
ENSG00000295991	ENST00000734864.1 link	n.48-30912A>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

191420

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

110756

African (AFR)

AF:

0.00

AC:

AN:

2964

American (AMR)

AF:

0.00

AC:

AN:

11392

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

4232

East Asian (EAS)

AF:

0.00

AC:

AN:

3150

South Asian (SAS)

AF:

0.00

AC:

AN:

37154

European-Finnish (FIN)

AF:

0.00

AC:

AN:

17300

Middle Eastern (MID)

AF:

0.00

AC:

AN:

702

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

105246

Other (OTH)

AF:

0.00

AC:

AN:

9280

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.7

(source)

DANN

Benign

0.40

PhyloP100

-0.051

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over