Genetic Variant ENSG00000299445:n.649+152C>T (chr6-54521183-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 ENST00000763589.1(ENSG00000299445):n.649+152C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,130 control chromosomes in the GnomAD database, including 1,269 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 0.10 ( 1269 hom., cov: 32)

Consequence

ENSG00000299445
ENST00000763589.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23

Publications

2 publications found

Variant links:

Genes affected

ENSG00000299445 (HGNC:):

ENSG00000299445 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299445	ENST00000763589.1 link	n.649+152C>T	intron_variant	Intron 5 of 6
ENSG00000299445	ENST00000763590.1 link	n.330-1026C>T	intron_variant	Intron 3 of 5
ENSG00000299445	ENST00000763594.1 link	n.328+152C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0999

AC:

15192

AN:

152012

Hom.:

1269

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0604

Gnomad ASJ

AF:

0.0510

Gnomad EAS

AF:

0.0143

Gnomad SAS

AF:

0.0147

Gnomad FIN

AF:

0.0256

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0562

Gnomad OTH

AF:

0.0852

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

GnomAD4 genome

AF:

0.100

AC:

15208

AN:

152130

Hom.:

1269

Cov.:

AF XY:

0.0950

AC XY:

7064

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.232

AC:

9637

AN:

41484

American (AMR)

AF:

0.0602

AC:

920

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0510

AC:

177

AN:

3472

East Asian (EAS)

AF:

0.0143

AC:

AN:

5160

South Asian (SAS)

AF:

0.0143

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0256

AC:

272

AN:

10606

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0562

AC:

3818

AN:

67990

Other (OTH)

AF:

0.0858

AC:

181

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

650

1299

1949

2598

3248

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

296

444

592

740

<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:

0.0888

Hom.:

126

Bravo

AF:

0.110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.28

(source)

DANN

Benign

0.65

PhyloP100

-1.2

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