Genetic Variant ENSG00000285336:n.251-4993G>T (chr3-180815463-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000485055.5(ENSG00000285336):n.251-4993G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,190 control chromosomes in the GnomAD database, including 49,064 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 0.80 ( 49064 hom., cov: 33)

Consequence

ENSG00000285336
ENST00000485055.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.584

Publications

7 publications found

Variant links:

Genes affected

ENSG00000285336 (HGNC:):

ENSG00000285336 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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928882	NR_109986.1 link	n.251-4993G>T		intron_variant	Intron 2 of 13

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000285336	ENST00000485055.5 link	n.251-4993G>T	intron_variant	Intron 2 of 13	1
ENSG00000145075	ENST00000471307.6 link	n.252+32044G>T	intron_variant	Intron 2 of 6	3
ENSG00000285336	ENST00000495817.1 link	n.207-33339G>T	intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.798

AC:

121338

AN:

152072

Hom.:

49020

Cov.:

show subpopulations

Gnomad AFR

AF:

0.937

Gnomad AMI

AF:

0.704

Gnomad AMR

AF:

0.776

Gnomad ASJ

AF:

0.688

Gnomad EAS

AF:

0.852

Gnomad SAS

AF:

0.721

Gnomad FIN

AF:

0.785

Gnomad MID

AF:

0.741

Gnomad NFE

AF:

0.730

Gnomad OTH

AF:

0.758

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

GnomAD4 genome

AF:

0.798

AC:

121436

AN:

152190

Hom.:

49064

Cov.:

AF XY:

0.799

AC XY:

59480

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.937

AC:

38931

AN:

41536

American (AMR)

AF:

0.776

AC:

11868

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.688

AC:

2385

AN:

3468

East Asian (EAS)

AF:

0.853

AC:

4408

AN:

5170

South Asian (SAS)

AF:

0.721

AC:

3473

AN:

4816

European-Finnish (FIN)

AF:

0.785

AC:

8305

AN:

10586

Middle Eastern (MID)

AF:

0.731

AC:

215

AN:

294

European-Non Finnish (NFE)

AF:

0.730

AC:

49616

AN:

68008

Other (OTH)

AF:

0.753

AC:

1594

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1239

2478

3716

4955

6194

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

874

1748

2622

3496

4370

<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:

0.747

Hom.:

183171

Bravo

AF:

0.805

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.53

(source)

DANN

Benign

0.31

PhyloP100

-0.58

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