Genetic Variant ENSG00000301530:n.139-3690G>A (chr11-69244671-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 ENST00000779509.1(ENSG00000301530):n.139-3690G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0677 in 152,214 control chromosomes in the GnomAD database, including 595 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 0.068 ( 595 hom., cov: 32)

Consequence

ENSG00000301530
ENST00000779509.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.30

Publications

2 publications found

Variant links:

Genes affected

ENSG00000301530 (HGNC:):

ENSG00000301530 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=-1.18).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 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
ENSG00000301530	ENST00000779509.1 link	n.139-3690G>A		intron_variant	Intron 1 of 3
ENSG00000301530	ENST00000779510.1 link	n.77-3690G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0677

AC:

10294

AN:

152096

Hom.:

594

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0130

Gnomad AMI

AF:

0.0746

Gnomad AMR

AF:

0.0912

Gnomad ASJ

AF:

0.0374

Gnomad EAS

AF:

0.220

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0696

Gnomad OTH

AF:

0.0574

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

GnomAD4 genome

AF:

0.0677

AC:

10299

AN:

152214

Hom.:

595

Cov.:

AF XY:

0.0735

AC XY:

5472

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.0130

AC:

538

AN:

41538

American (AMR)

AF:

0.0917

AC:

1403

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0374

AC:

130

AN:

3472

East Asian (EAS)

AF:

0.220

AC:

1141

AN:

5182

South Asian (SAS)

AF:

0.101

AC:

486

AN:

4824

European-Finnish (FIN)

AF:

0.158

AC:

1667

AN:

10572

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0696

AC:

4736

AN:

68000

Other (OTH)

AF:

0.0582

AC:

123

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

471

942

1414

1885

2356

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.0720

Hom.:

381

Bravo

AF:

0.0606

Asia WGS

AF:

0.160

AC:

555

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.2

CADD

Benign

0.16

(source)

DANN

Benign

0.66

PhyloP100

-4.3

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