Genetic Variant ENST00000506077.1:n.65T>C (chr4-10285644-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000506077.1(ENSG00000250505):n.65T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 152,112 control chromosomes in the GnomAD database, including 30,654 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 0.63 ( 30629 hom., cov: 32)

Exomes 𝑓: 0.72 ( 25 hom. )

Consequence

ENSG00000250505
ENST00000506077.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0900

Publications

7 publications found

Variant links:

Genes affected

ENSG00000250505 (HGNC:):

ENSG00000250505 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 (NFE) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100422637		n.10285644A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250505	ENST00000506077.1 link	n.65T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.631

AC:

95793

AN:

151890

Hom.:

30609

Cov.:

show subpopulations

Gnomad AFR

AF:

0.538

Gnomad AMI

AF:

0.587

Gnomad AMR

AF:

0.618

Gnomad ASJ

AF:

0.586

Gnomad EAS

AF:

0.540

Gnomad SAS

AF:

0.683

Gnomad FIN

AF:

0.693

Gnomad MID

AF:

0.547

Gnomad NFE

AF:

0.687

Gnomad OTH

AF:

0.623

GnomAD4 exome

AF:

0.721

AC:

AN:

104

Hom.:

Cov.:

AF XY:

0.729

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.625

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.721

AC:

AN:

Other (OTH)

AF:

0.833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

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:

0.631

AC:

95862

AN:

152008

Hom.:

30629

Cov.:

AF XY:

0.632

AC XY:

46962

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.538

AC:

22305

AN:

41450

American (AMR)

AF:

0.619

AC:

9442

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.586

AC:

2034

AN:

3470

East Asian (EAS)

AF:

0.540

AC:

2784

AN:

5154

South Asian (SAS)

AF:

0.683

AC:

3291

AN:

4818

European-Finnish (FIN)

AF:

0.693

AC:

7336

AN:

10588

Middle Eastern (MID)

AF:

0.544

AC:

160

AN:

294

European-Non Finnish (NFE)

AF:

0.687

AC:

46672

AN:

67958

Other (OTH)

AF:

0.618

AC:

1306

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1774

3549

5323

7098

8872

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

790

1580

2370

3160

3950

<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:

0.606

Hom.:

3336

Bravo

AF:

0.616

Asia WGS

AF:

0.634

AC:

2204

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.1

(source)

DANN

Benign

0.58

PhyloP100

-0.090

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