Genetic Variant ENSG00000230628:n.97-7818C>G (chr1-234680808-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 ENST00000442382.1(ENSG00000230628):n.97-7818C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,762 control chromosomes in the GnomAD database, including 26,460 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 0.58 ( 26404 hom., cov: 28)

Exomes 𝑓: 0.61 ( 56 hom. )

Consequence

ENSG00000230628
ENST00000442382.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.590

Publications

11 publications found

Variant links:

Genes affected

ENSG00000230628 (HGNC:):

ENSG00000230628 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373209	NR_188651.1 link	n.123-3G>C		splice_region_variant, intron_variant	Intron 1 of 2
LOC105373208	XR_949287.4 link	n.446-1459C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000230628	ENST00000442382.1 link	n.97-7818C>G	intron_variant	Intron 1 of 1	2
ENSG00000228044	ENST00000449012.2 link	n.313-3G>C	splice_region_variant, intron_variant	Intron 2 of 2	3
ENSG00000228044	ENST00000453568.1 link	n.32-3G>C	splice_region_variant, intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.580

AC:

87806

AN:

151374

Hom.:

26374

Cov.:

show subpopulations

Gnomad AFR

AF:

0.672

Gnomad AMI

AF:

0.471

Gnomad AMR

AF:

0.464

Gnomad ASJ

AF:

0.528

Gnomad EAS

AF:

0.165

Gnomad SAS

AF:

0.438

Gnomad FIN

AF:

0.540

Gnomad MID

AF:

0.564

Gnomad NFE

AF:

0.602

Gnomad OTH

AF:

0.571

GnomAD4 exome

AF:

0.611

AC:

165

AN:

270

Hom.:

Cov.:

AF XY:

0.610

AC XY:

100

AN XY:

164

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.750

AC:

AN:

European-Finnish (FIN)

AF:

0.488

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.675

AC:

104

AN:

154

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.536

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.580

AC:

87877

AN:

151492

Hom.:

26404

Cov.:

AF XY:

0.569

AC XY:

42104

AN XY:

73970

show subpopulations

African (AFR)

AF:

0.673

AC:

27746

AN:

41256

American (AMR)

AF:

0.463

AC:

7056

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.528

AC:

1829

AN:

3462

East Asian (EAS)

AF:

0.165

AC:

842

AN:

5112

South Asian (SAS)

AF:

0.439

AC:

2105

AN:

4796

European-Finnish (FIN)

AF:

0.540

AC:

5662

AN:

10478

Middle Eastern (MID)

AF:

0.565

AC:

165

AN:

292

European-Non Finnish (NFE)

AF:

0.602

AC:

40849

AN:

67832

Other (OTH)

AF:

0.565

AC:

1193

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1746

3491

5237

6982

8728

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

738

1476

2214

2952

3690

<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.:

14385

Bravo

AF:

0.580

Asia WGS

AF:

0.305

AC:

1065

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.85

(source)

DANN

Benign

0.64

PhyloP100

0.59

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