ENST00000437082.5:n.*224-1263G>A – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000437082.5(ENSG00000272410):n.*224-1263G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 152,074 control chromosomes in the GnomAD database, including 32,399 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 0.64 ( 32385 hom., cov: 31)

Exomes 𝑓: 0.61 ( 14 hom. )

Consequence

ENSG00000272410
ENST00000437082.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.290

Publications

25 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000437082.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
LINC00852	NR_026829.1	n.67G>A	non_coding_transcript_exon	Exon 1 of 1
GHRLOS	NR_004431.3	n.52-1263G>A	intron	N/A
GHRLOS	NR_024144.2	n.134+882G>A	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ENSG00000272410	ENST00000437082.5	TSL:2	n.*224-1263G>A	intron	N/A	ENSP00000402783.1
LINC00852	ENST00000475197.1	TSL:6	n.67G>A	non_coding_transcript_exon	Exon 1 of 1
LINC00852	ENST00000538717.1	TSL:6	n.67G>A	non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.640

AC:

97201

AN:

151892

Hom.:

32346

Cov.:

show subpopulations

Gnomad AFR

AF:

0.775

Gnomad AMI

AF:

0.599

Gnomad AMR

AF:

0.709

Gnomad ASJ

AF:

0.592

Gnomad EAS

AF:

0.955

Gnomad SAS

AF:

0.818

Gnomad FIN

AF:

0.540

Gnomad MID

AF:

0.636

Gnomad NFE

AF:

0.525

Gnomad OTH

AF:

0.617

GnomAD4 exome

AF:

0.609

AC:

AN:

Hom.:

Cov.:

AF XY:

0.640

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.125

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.605

AC:

AN:

Other (OTH)

AF:

0.700

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.640

AC:

97299

AN:

152010

Hom.:

32385

Cov.:

AF XY:

0.649

AC XY:

48184

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.775

AC:

32127

AN:

41462

American (AMR)

AF:

0.710

AC:

10838

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.592

AC:

2056

AN:

3472

East Asian (EAS)

AF:

0.955

AC:

4934

AN:

5166

South Asian (SAS)

AF:

0.817

AC:

3934

AN:

4818

European-Finnish (FIN)

AF:

0.540

AC:

5699

AN:

10544

Middle Eastern (MID)

AF:

0.639

AC:

188

AN:

294

European-Non Finnish (NFE)

AF:

0.525

AC:

35680

AN:

67966

Other (OTH)

AF:

0.615

AC:

1297

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1667

3334

5002

6669

8336

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

782

1564

2346

3128

3910

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.570

Hom.:

72875

Bravo

AF:

0.656

Asia WGS

AF:

0.845

AC:

2936

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.5

(source)

DANN

Benign

0.76

PhyloP100

-0.29

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over