Genetic Variant ENSG00000299691:n.92-33894A>T (chr14-38551301-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000765620.1(ENSG00000299691):n.92-33894A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0643 in 152,232 control chromosomes in the GnomAD database, including 692 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 0.064 ( 692 hom., cov: 32)

Consequence

ENSG00000299691
ENST00000765620.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.179

Publications

9 publications found

Variant links:

Genes affected

ENSG00000299691 (HGNC:):

ENSG00000299691 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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299691	ENST00000765620.1 link	n.92-33894A>T	intron_variant	Intron 1 of 3
ENSG00000299691	ENST00000765621.1 link	n.87-1295A>T	intron_variant	Intron 1 of 3
ENSG00000299691	ENST00000765622.1 link	n.54+16536A>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0644

AC:

9792

AN:

152114

Hom.:

691

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.135

Gnomad ASJ

AF:

0.0109

Gnomad EAS

AF:

0.203

Gnomad SAS

AF:

0.0551

Gnomad FIN

AF:

0.0255

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00300

Gnomad OTH

AF:

0.0521

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

GnomAD4 genome

AF:

0.0643

AC:

9796

AN:

152232

Hom.:

692

Cov.:

AF XY:

0.0686

AC XY:

5104

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.140

AC:

5798

AN:

41540

American (AMR)

AF:

0.135

AC:

2060

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0109

AC:

AN:

3472

East Asian (EAS)

AF:

0.203

AC:

1048

AN:

5162

South Asian (SAS)

AF:

0.0547

AC:

264

AN:

4826

European-Finnish (FIN)

AF:

0.0255

AC:

271

AN:

10614

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00300

AC:

204

AN:

68026

Other (OTH)

AF:

0.0520

AC:

110

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

419

839

1258

1678

2097

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<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:

0.0195

Hom.:

136

Bravo

AF:

0.0764

Asia WGS

AF:

0.123

AC:

427

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

3.0

(source)

DANN

Benign

0.70

PhyloP100

0.18

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