Genetic Variant ENSG00000300301:n.405+3566T>C (chr17-17402773-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000770697.1(ENSG00000300301):n.405+3566T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,156 control chromosomes in the GnomAD database, including 1,888 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 0.15 ( 1888 hom., cov: 32)

Consequence

ENSG00000300301
ENST00000770697.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.57

Publications

5 publications found

Variant links:

Genes affected

ENSG00000300301 (HGNC:):

ENSG00000300301 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=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 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
ENSG00000300301	ENST00000770697.1 link	n.405+3566T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

22885

AN:

152038

Hom.:

1875

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.106

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.168

Gnomad EAS

AF:

0.116

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.0889

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.147

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

GnomAD4 genome

AF:

0.151

AC:

22934

AN:

152156

Hom.:

1888

Cov.:

AF XY:

0.148

AC XY:

11018

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.226

AC:

9395

AN:

41496

American (AMR)

AF:

0.128

AC:

1959

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.168

AC:

583

AN:

3468

East Asian (EAS)

AF:

0.116

AC:

603

AN:

5184

South Asian (SAS)

AF:

0.152

AC:

731

AN:

4820

European-Finnish (FIN)

AF:

0.0889

AC:

943

AN:

10606

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.122

AC:

8273

AN:

67984

Other (OTH)

AF:

0.145

AC:

307

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

964

1929

2893

3858

4822

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

258

516

774

1032

1290

<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:

0.134

Hom.:

1396

Bravo

AF:

0.157

Asia WGS

AF:

0.150

AC:

523

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

0.62

(source)

DANN

Benign

0.33

PhyloP100

-1.6

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