dbSNP rs10407714: ENSG00000290821:n.4417G>A (chr19-9208547-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 ENST00000641088.1(ENSG00000290821):n.4417G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,078 control chromosomes in the GnomAD database, including 8,940 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 0.26 ( 8940 hom., cov: 32)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

ENSG00000290821
ENST00000641088.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.547

Publications

3 publications found

Variant links:

Genes affected

ENSG00000290821 (HGNC:):

ENSG00000290821 links:

OR7E24 (HGNC:8396): (olfactory receptor family 7 subfamily E member 24) 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]

OR7E24 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR7E24	XM_047438594.1 link	c.32+1525G>A		intron_variant	Intron 1 of 2		XP_047294550.1
OR7E24	XM_047438597.1 link	c.-207+1525G>A		intron_variant	Intron 1 of 3		XP_047294553.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290821	ENST00000641088.1 link	n.4417G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39170

AN:

151956

Hom.:

8890

Cov.:

show subpopulations

Gnomad AFR

AF:

0.613

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.245

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.0881

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.100

Gnomad OTH

AF:

0.226

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

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)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AC:

AN:

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.275

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.258

AC:

39275

AN:

152074

Hom.:

8940

Cov.:

AF XY:

0.258

AC XY:

19164

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.614

AC:

25462

AN:

41452

American (AMR)

AF:

0.153

AC:

2332

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

571

AN:

3464

East Asian (EAS)

AF:

0.244

AC:

1266

AN:

5178

South Asian (SAS)

AF:

0.273

AC:

1315

AN:

4822

European-Finnish (FIN)

AF:

0.0881

AC:

933

AN:

10588

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.100

AC:

6814

AN:

67982

Other (OTH)

AF:

0.227

AC:

480

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1088

2176

3265

4353

5441

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

354

708

1062

1416

1770

<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:

0.156

Hom.:

6232

Bravo

AF:

0.279

Asia WGS

AF:

0.261

AC:

909

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.48

(source)

DANN

Benign

0.61

PhyloP100

-0.55

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over