Genetic Variant ENSG00000285838:n.418-40005G>A (chr6-68182664-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000718116.1(ENSG00000285838):n.418-40005G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,864 control chromosomes in the GnomAD database, including 11,110 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 0.35 ( 11110 hom., cov: 32)

Consequence

ENSG00000285838
ENST00000718116.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Publications

5 publications found

Variant links:

Genes affected

ENSG00000285838 (HGNC:):

ENSG00000285838 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.29).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 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
ENSG00000285838	ENST00000718116.1 link	n.418-40005G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.350

AC:

53118

AN:

151746

Hom.:

11108

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.432

Gnomad AMR

AF:

0.406

Gnomad ASJ

AF:

0.451

Gnomad EAS

AF:

0.532

Gnomad SAS

AF:

0.329

Gnomad FIN

AF:

0.430

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.455

Gnomad OTH

AF:

0.399

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

GnomAD4 genome

AF:

0.350

AC:

53121

AN:

151864

Hom.:

11110

Cov.:

AF XY:

0.352

AC XY:

26121

AN XY:

74192

show subpopulations

African (AFR)

AF:

0.103

AC:

4253

AN:

41446

American (AMR)

AF:

0.406

AC:

6183

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.451

AC:

1564

AN:

3466

East Asian (EAS)

AF:

0.532

AC:

2730

AN:

5132

South Asian (SAS)

AF:

0.329

AC:

1583

AN:

4812

European-Finnish (FIN)

AF:

0.430

AC:

4542

AN:

10556

Middle Eastern (MID)

AF:

0.479

AC:

140

AN:

292

European-Non Finnish (NFE)

AF:

0.455

AC:

30901

AN:

67912

Other (OTH)

AF:

0.396

AC:

834

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1645

3290

4934

6579

8224

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

506

1012

1518

2024

2530

<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:

0.424

Hom.:

7252

Bravo

AF:

0.343

Asia WGS

AF:

0.385

AC:

1340

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

1.1

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