dbSNP rs171407: ENSG00000272410:n.*224-1263G>A (chr3-10284485-G-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.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ENSG00000272410	ENST00000437082.5 link	n.*224-1263G>A	intron_variant	Intron 7 of 7	2	ENSP00000402783.1	H7C1W4
LINC00852	ENST00000475197.1 link	n.67G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC00852	ENST00000538717.1 link	n.67G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000272410	ENST00000450534.1 link	n.*2447-1263G>A	intron_variant	Intron 7 of 7	2	ENSP00000399689.1	H7C1D0

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over