dbSNP rs4988822: ENSG00000299747:n.280-467G>A (chr6-32431198-C-T) – 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.280-467G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 150,502 control chromosomes in the GnomAD database, including 4,937 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 0.23 ( 4937 hom., cov: 31)

Consequence

ENSG00000299747
ENST00000766007.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.194

Publications

11 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299747	ENST00000766007.1 link	n.280-467G>A	intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766247.1 link	n.283-2894C>T	intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1 link	n.*190C>T	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.234

AC:

35264

AN:

150386

Hom.:

4935

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.323

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.158

Gnomad SAS

AF:

0.170

Gnomad FIN

AF:

0.409

Gnomad MID

AF:

0.100

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.232

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

GnomAD4 genome

AF:

0.234

AC:

35286

AN:

150502

Hom.:

4937

Cov.:

AF XY:

0.237

AC XY:

17402

AN XY:

73502

show subpopulations

African (AFR)

AF:

0.143

AC:

5906

AN:

41160

American (AMR)

AF:

0.206

AC:

3117

AN:

15098

Ashkenazi Jewish (ASJ)

AF:

0.145

AC:

500

AN:

3448

East Asian (EAS)

AF:

0.158

AC:

813

AN:

5148

South Asian (SAS)

AF:

0.171

AC:

817

AN:

4768

European-Finnish (FIN)

AF:

0.409

AC:

4248

AN:

10374

Middle Eastern (MID)

AF:

0.0972

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.284

AC:

19086

AN:

67224

Other (OTH)

AF:

0.229

AC:

480

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1253

2505

3758

5010

6263

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:

0.241

Hom.:

2145

Bravo

AF:

0.220

Asia WGS

AF:

0.203

AC:

710

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.5

(source)

DANN

Benign

0.46

PhyloP100

-0.19

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