Genetic Variant ENSG00000303969:n.254+39T>C (chr5-148824199-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000798472.1(ENSG00000303969):n.254+39T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,064 control chromosomes in the GnomAD database, including 27,690 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 0.60 ( 27690 hom., cov: 33)

Consequence

ENSG00000303969
ENST00000798472.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.511

Publications

18 publications found

Variant links:

Genes affected

ENSG00000303969 (HGNC:):

ENSG00000303969 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 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
ENSG00000303969	ENST00000798472.1 link	n.254+39T>C		intron_variant	Intron 2 of 4
ENSG00000303969	ENST00000798473.1 link	n.251+39T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.599

AC:

90958

AN:

151946

Hom.:

27671

Cov.:

show subpopulations

Gnomad AFR

AF:

0.564

Gnomad AMI

AF:

0.556

Gnomad AMR

AF:

0.710

Gnomad ASJ

AF:

0.613

Gnomad EAS

AF:

0.746

Gnomad SAS

AF:

0.740

Gnomad FIN

AF:

0.632

Gnomad MID

AF:

0.731

Gnomad NFE

AF:

0.567

Gnomad OTH

AF:

0.625

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

GnomAD4 genome

AF:

0.599

AC:

91022

AN:

152064

Hom.:

27690

Cov.:

AF XY:

0.606

AC XY:

45036

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.563

AC:

23369

AN:

41478

American (AMR)

AF:

0.711

AC:

10869

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.613

AC:

2127

AN:

3472

East Asian (EAS)

AF:

0.745

AC:

3854

AN:

5170

South Asian (SAS)

AF:

0.741

AC:

3570

AN:

4818

European-Finnish (FIN)

AF:

0.632

AC:

6683

AN:

10572

Middle Eastern (MID)

AF:

0.731

AC:

215

AN:

294

European-Non Finnish (NFE)

AF:

0.567

AC:

38500

AN:

67946

Other (OTH)

AF:

0.630

AC:

1329

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1884

3767

5651

7534

9418

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

756

1512

2268

3024

3780

<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:

0.575

Hom.:

3527

Bravo

AF:

0.600

Asia WGS

AF:

0.748

AC:

2588

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

(source)

DANN

Benign

0.74

PhyloP100

-0.51

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