Genetic Variant ENSG00000272410:n.*224-1263G>T (chr3-10284485-G-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 ENST00000437082.5(ENSG00000272410):n.*224-1263G>T variant causes a intron 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: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ENSG00000272410
ENST00000437082.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.290

Publications

0 publications found

Variant links:

Genes affected

ENSG00000272410 (HGNC:):

ENSG00000272410 links:

LINC00852 (HGNC:29904): (long intergenic non-protein coding RNA 852)

LINC00852 links:

GHRLOS (HGNC:33885): (ghrelin opposite strand/antisense RNA) This gene is an antisense gene of the ghrelin/obestatin prepropeptide gene. Alternatively spliced transcript variants have been identified and they may function as non-coding regulatory RNAs. [provided by RefSeq, Jan 2013]

GHRLOS 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=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00852	NR_026829.1 link	n.67G>T	non_coding_transcript_exon_variant	Exon 1 of 1
GHRLOS	NR_004431.3 link	n.52-1263G>T	intron_variant	Intron 1 of 4
GHRLOS	NR_024144.2 link	n.134+882G>T	intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
ENSG00000272410	ENST00000437082.5 link	n.*224-1263G>T	intron_variant	Intron 7 of 7	2	ENSP00000402783.1
LINC00852	ENST00000475197.1 link	n.67G>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC00852	ENST00000538717.1 link	n.67G>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000272410	ENST00000450534.1 link	n.*2447-1263G>T	intron_variant	Intron 7 of 7	2	ENSP00000399689.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.40

(source)

DANN

Benign

0.78

PhyloP100

-0.29

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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