Genetic Variant ENST00000619867.4:n.701-37110A>G (chr1-147445799-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000619867.4(LINC00624):n.701-37110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,006 control chromosomes in the GnomAD database, including 39,245 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 0.71 ( 39245 hom., cov: 31)

Exomes 𝑓: 0.65 ( 8 hom. )

Failed GnomAD Quality Control

Consequence

LINC00624
ENST00000619867.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.213

Publications

2 publications found

Variant links:

Genes affected

LINC00624 (HGNC:44254): (long intergenic non-protein coding RNA 624)

LINC00624 links:

OR13Z2P (HGNC:31241): (olfactory receptor family 13 subfamily Z member 2 pseudogene) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

OR13Z2P links:

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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=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619867.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00624	NR_038423.2		n.701-60936A>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC00624	ENST00000619867.4	TSL:1	n.701-37110A>G	intron	N/A
LINC00624	ENST00000621316.2	TSL:1	n.705-60936A>G	intron	N/A
OR13Z2P	ENST00000606338.1	TSL:6	n.221T>C	non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.708

AC:

107547

AN:

151888

Hom.:

39175

Cov.:

show subpopulations

Gnomad AFR

AF:

0.891

Gnomad AMI

AF:

0.709

Gnomad AMR

AF:

0.727

Gnomad ASJ

AF:

0.497

Gnomad EAS

AF:

0.599

Gnomad SAS

AF:

0.615

Gnomad FIN

AF:

0.684

Gnomad MID

AF:

0.614

Gnomad NFE

AF:

0.623

Gnomad OTH

AF:

0.670

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.650

AC:

AN:

Hom.:

Cov.:

AF XY:

0.636

AC XY:

AN XY:

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:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.647

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.535

Heterozygous variant carriers

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:

0.708

AC:

107679

AN:

152006

Hom.:

39245

Cov.:

AF XY:

0.709

AC XY:

52640

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.891

AC:

36994

AN:

41504

American (AMR)

AF:

0.727

AC:

11111

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.497

AC:

1725

AN:

3472

East Asian (EAS)

AF:

0.599

AC:

3073

AN:

5132

South Asian (SAS)

AF:

0.617

AC:

2960

AN:

4800

European-Finnish (FIN)

AF:

0.684

AC:

7225

AN:

10560

Middle Eastern (MID)

AF:

0.619

AC:

182

AN:

294

European-Non Finnish (NFE)

AF:

0.623

AC:

42349

AN:

67940

Other (OTH)

AF:

0.668

AC:

1413

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1493

2986

4479

5972

7465

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

808

1616

2424

3232

4040

<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:

0.631

Hom.:

3229

Bravo

AF:

0.722

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

5.3

(source)

PhyloP100

0.21

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over