Genetic Variant ENSG00000303547:n.175+29035C>G (chr4-99792608-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 ENST00000795494.1(ENSG00000303547):n.175+29035C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,948 control chromosomes in the GnomAD database, including 8,584 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 0.33 ( 8584 hom., cov: 31)

Consequence

ENSG00000303547
ENST00000795494.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33

Publications

9 publications found

Variant links:

Genes affected

ENSG00000303547 (HGNC:):

ENSG00000303547 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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
ENSG00000303547	ENST00000795494.1 link	n.175+29035C>G		intron_variant	Intron 2 of 2
ENSG00000303547	ENST00000795495.1 link	n.349+29035C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.331

AC:

50305

AN:

151832

Hom.:

8566

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.387

Gnomad ASJ

AF:

0.400

Gnomad EAS

AF:

0.392

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.382

Gnomad NFE

AF:

0.361

Gnomad OTH

AF:

0.374

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

GnomAD4 genome

AF:

0.331

AC:

50368

AN:

151948

Hom.:

8584

Cov.:

AF XY:

0.327

AC XY:

24291

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.278

AC:

11506

AN:

41436

American (AMR)

AF:

0.387

AC:

5912

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.400

AC:

1385

AN:

3464

East Asian (EAS)

AF:

0.393

AC:

2032

AN:

5170

South Asian (SAS)

AF:

0.206

AC:

994

AN:

4822

European-Finnish (FIN)

AF:

0.264

AC:

2787

AN:

10540

Middle Eastern (MID)

AF:

0.380

AC:

111

AN:

292

European-Non Finnish (NFE)

AF:

0.361

AC:

24524

AN:

67934

Other (OTH)

AF:

0.376

AC:

794

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1703

3406

5108

6811

8514

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

486

972

1458

1944

2430

<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:

0.338

Hom.:

1084

Bravo

AF:

0.341

Asia WGS

AF:

0.292

AC:

1016

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.17

(source)

DANN

Benign

0.45

PhyloP100

-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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