Genetic Variant ENSG00000301554:n.629+5051C>G (chr4-6889792-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000779681.1(ENSG00000301554):n.629+5051C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,220 control chromosomes in the GnomAD database, including 2,742 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 0.17 ( 2742 hom., cov: 33)

Consequence

ENSG00000301554
ENST00000779681.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.361

Publications

21 publications found

Variant links:

Genes affected

ENSG00000301554 (HGNC:):

ENSG00000301554 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 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
ENSG00000301554	ENST00000779681.1 link	n.629+5051C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26287

AN:

152104

Hom.:

2742

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.124

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.557

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.193

Gnomad MID

AF:

0.150

Gnomad NFE

AF:

0.175

Gnomad OTH

AF:

0.178

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

GnomAD4 genome

AF:

0.173

AC:

26284

AN:

152220

Hom.:

2742

Cov.:

AF XY:

0.174

AC XY:

12960

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.112

AC:

4651

AN:

41554

American (AMR)

AF:

0.202

AC:

3096

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

407

AN:

3470

East Asian (EAS)

AF:

0.557

AC:

2873

AN:

5162

South Asian (SAS)

AF:

0.169

AC:

816

AN:

4826

European-Finnish (FIN)

AF:

0.193

AC:

2049

AN:

10606

Middle Eastern (MID)

AF:

0.151

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.175

AC:

11865

AN:

67984

Other (OTH)

AF:

0.175

AC:

370

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1105

2210

3316

4421

5526

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

294

588

882

1176

1470

<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:

0.185

Hom.:

1722

Bravo

AF:

0.175

Asia WGS

AF:

0.266

AC:

926

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.8

(source)

DANN

Benign

0.63

PhyloP100

0.36

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