Genetic Variant ENST00000752301.1:n.80+13624C>G (chr7-64357509-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000752301.1(ENSG00000287699):n.80+13624C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,036 control chromosomes in the GnomAD database, including 1,259 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 0.12 ( 1259 hom., cov: 31)

Consequence

ENSG00000287699
ENST00000752301.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0790

Publications

2 publications found

Variant links:

Genes affected

ENSG00000287699 (HGNC:):

ENSG00000287699 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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 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
ENSG00000287699	ENST00000752301.1 link	n.80+13624C>G		intron_variant	Intron 1 of 2
ENSG00000287699	ENST00000752302.1 link	n.50+13624C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17785

AN:

151920

Hom.:

1259

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0518

Gnomad AMI

AF:

0.122

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.121

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

GnomAD4 genome

AF:

0.117

AC:

17786

AN:

152036

Hom.:

1259

Cov.:

AF XY:

0.114

AC XY:

8503

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.0518

AC:

2151

AN:

41516

American (AMR)

AF:

0.130

AC:

1982

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.120

AC:

415

AN:

3472

East Asian (EAS)

AF:

0.000195

AC:

AN:

5116

South Asian (SAS)

AF:

0.111

AC:

533

AN:

4810

European-Finnish (FIN)

AF:

0.134

AC:

1419

AN:

10582

Middle Eastern (MID)

AF:

0.120

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.160

AC:

10887

AN:

67948

Other (OTH)

AF:

0.119

AC:

252

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

792

1584

2377

3169

3961

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

190

380

570

760

950

<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:

0.0766

Hom.:

110

Bravo

AF:

0.112

Asia WGS

AF:

0.0590

AC:

204

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.6

(source)

DANN

Benign

0.73

PhyloP100

0.079

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