Genetic Variant ENSG00000284642:n.*120T>C (chr1-10397483-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 ENST00000641062.1(ENSG00000284642):n.*120T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,040 control chromosomes in the GnomAD database, including 8,441 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 ( 8440 hom., cov: 32)

Exomes 𝑓: 0.38 ( 1 hom. )

Consequence

ENSG00000284642
ENST00000641062.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.703

Publications

5 publications found

Variant links:

Genes affected

ENSG00000284642 (HGNC:):

ENSG00000284642 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=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000284642	ENST00000641062.1 link	n.*120T>C	downstream_gene_variant
ENSG00000284642	ENST00000641335.1 link	n.*51T>C	downstream_gene_variant
ENSG00000284642	ENST00000641456.1 link	n.*107T>C	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.330

AC:

50149

AN:

151914

Hom.:

8409

Cov.:

show subpopulations

Gnomad AFR

AF:

0.327

Gnomad AMI

AF:

0.475

Gnomad AMR

AF:

0.369

Gnomad ASJ

AF:

0.324

Gnomad EAS

AF:

0.357

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.345

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.321

Gnomad OTH

AF:

0.330

GnomAD4 exome

AF:

0.375

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.375

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.725

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.330

AC:

50230

AN:

152032

Hom.:

8440

Cov.:

AF XY:

0.331

AC XY:

24622

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.327

AC:

13557

AN:

41462

American (AMR)

AF:

0.370

AC:

5639

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.324

AC:

1122

AN:

3468

East Asian (EAS)

AF:

0.358

AC:

1850

AN:

5172

South Asian (SAS)

AF:

0.278

AC:

1338

AN:

4816

European-Finnish (FIN)

AF:

0.345

AC:

3647

AN:

10560

Middle Eastern (MID)

AF:

0.381

AC:

112

AN:

294

European-Non Finnish (NFE)

AF:

0.321

AC:

21824

AN:

67976

Other (OTH)

AF:

0.335

AC:

708

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1772

3544

5315

7087

8859

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<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:

0.328

Hom.:

8691

Bravo

AF:

0.335

Asia WGS

AF:

0.349

AC:

1211

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.5

(source)

DANN

Benign

0.64

PhyloP100

-0.70

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over