Genetic Variant ENSG00000272410:n.*224-746A>G (chr3-10285002-A-G) – 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.*224-746A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 153,804 control chromosomes in the GnomAD database, including 6,637 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 0.28 ( 6610 hom., cov: 33)

Exomes 𝑓: 0.22 ( 27 hom. )

Consequence

ENSG00000272410
ENST00000437082.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.48

Publications

26 publications found

Variant links:

COSMIC-nc: COSV55051957

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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 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.584A>G	non_coding_transcript_exon	Exon 1 of 1
GHRLOS	NR_004431.3	n.52-746A>G	intron	N/A
GHRLOS	NR_024144.2	n.135-746A>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ENSG00000272410	ENST00000437082.5	TSL:2	n.*224-746A>G	intron	N/A	ENSP00000402783.1
LINC00852	ENST00000475197.1	TSL:6	n.584A>G	non_coding_transcript_exon	Exon 1 of 1
LINC00852	ENST00000538717.1	TSL:6	n.584A>G	non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

43286

AN:

152088

Hom.:

6597

Cov.:

show subpopulations

Gnomad AFR

AF:

0.373

Gnomad AMI

AF:

0.448

Gnomad AMR

AF:

0.210

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.0260

Gnomad SAS

AF:

0.225

Gnomad FIN

AF:

0.210

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.288

GnomAD4 exome

AF:

0.217

AC:

346

AN:

1598

Hom.:

Cov.:

AF XY:

0.203

AC XY:

170

AN XY:

838

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.213

AC:

329

AN:

1546

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.344

AC:

AN:

Other (OTH)

AF:

0.300

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

103

129

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.285

AC:

43342

AN:

152206

Hom.:

6610

Cov.:

AF XY:

0.279

AC XY:

20758

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.373

AC:

15486

AN:

41492

American (AMR)

AF:

0.210

AC:

3213

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.315

AC:

1093

AN:

3470

East Asian (EAS)

AF:

0.0258

AC:

134

AN:

5186

South Asian (SAS)

AF:

0.226

AC:

1093

AN:

4828

European-Finnish (FIN)

AF:

0.210

AC:

2231

AN:

10612

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.279

AC:

19002

AN:

67996

Other (OTH)

AF:

0.284

AC:

600

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1564

3127

4691

6254

7818

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

436

872

1308

1744

2180

<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:

0.261

Hom.:

3224

Bravo

AF:

0.287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.015

(source)

DANN

Benign

0.26

PhyloP100

-2.5

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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