dbSNP rs7762370: ENSG00000299747:n.280-1682A>G (chr6-32432413-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 ENST00000766007.1(ENSG00000299747):n.280-1682A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0707 in 152,258 control chromosomes in the GnomAD database, including 546 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 0.071 ( 546 hom., cov: 32)

Consequence

ENSG00000299747
ENST00000766007.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.90

Publications

8 publications found

Variant links:

Genes affected

ENSG00000299747 (HGNC:):

ENSG00000299747 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299747	ENST00000766007.1 link	n.280-1682A>G		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766247.1 link	n.283-1679T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0707

AC:

10752

AN:

152140

Hom.:

546

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.0371

Gnomad ASJ

AF:

0.0213

Gnomad EAS

AF:

0.00828

Gnomad SAS

AF:

0.0600

Gnomad FIN

AF:

0.0163

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0512

Gnomad OTH

AF:

0.0656

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0707

AC:

10767

AN:

152258

Hom.:

546

Cov.:

AF XY:

0.0681

AC XY:

5072

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.140

AC:

5820

AN:

41538

American (AMR)

AF:

0.0371

AC:

567

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0213

AC:

AN:

3468

East Asian (EAS)

AF:

0.00829

AC:

AN:

5184

South Asian (SAS)

AF:

0.0594

AC:

287

AN:

4832

European-Finnish (FIN)

AF:

0.0163

AC:

173

AN:

10616

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0512

AC:

3485

AN:

68012

Other (OTH)

AF:

0.0649

AC:

137

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

492

984

1475

1967

2459

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

224

336

448

560

<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:

0.0581

Hom.:

499

Bravo

AF:

0.0759

Asia WGS

AF:

0.0280

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.7

(source)

DANN

Benign

0.85

PhyloP100

1.9

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over