Genetic Variant ENST00000436042.2:n.16T>C (chr7-56483270-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 ENST00000436042.2(ENSG00000225488):n.16T>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 0.852 in 152,266 control chromosomes in the GnomAD database, including 55,701 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 0.85 ( 55666 hom., cov: 31)

Exomes 𝑓: 0.84 ( 35 hom. )

Consequence

ENSG00000225488
ENST00000436042.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.875

Publications

7 publications found

Variant links:

Genes affected

ENSG00000225488 (HGNC:):

ENSG00000225488 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100240728	NR_108095.1 link	n.50T>C		non_coding_transcript_exon_variant	Exon 1 of 2
LOC124901640	XR_007060331.1 link	n.148A>G		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000225488	ENST00000436042.2 link	n.16T>C	non_coding_transcript_exon_variant	Exon 1 of 2	1
ENSG00000225488	ENST00000651867.3 link	n.61T>C	non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000225488	ENST00000665097.1 link	n.13T>C	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.852

AC:

129494

AN:

152050

Hom.:

55611

Cov.:

show subpopulations

Gnomad AFR

AF:

0.949

Gnomad AMI

AF:

0.910

Gnomad AMR

AF:

0.888

Gnomad ASJ

AF:

0.864

Gnomad EAS

AF:

0.606

Gnomad SAS

AF:

0.887

Gnomad FIN

AF:

0.716

Gnomad MID

AF:

0.886

Gnomad NFE

AF:

0.819

Gnomad OTH

AF:

0.862

GnomAD4 exome

AF:

0.837

AC:

AN:

Hom.:

Cov.:

AF XY:

0.803

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

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:

0.667

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.911

AC:

AN:

Other (OTH)

AF:

0.900

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.852

AC:

129604

AN:

152168

Hom.:

55666

Cov.:

AF XY:

0.848

AC XY:

63097

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.949

AC:

39428

AN:

41548

American (AMR)

AF:

0.888

AC:

13588

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.864

AC:

2999

AN:

3472

East Asian (EAS)

AF:

0.606

AC:

3117

AN:

5140

South Asian (SAS)

AF:

0.887

AC:

4279

AN:

4824

European-Finnish (FIN)

AF:

0.716

AC:

7568

AN:

10570

Middle Eastern (MID)

AF:

0.891

AC:

262

AN:

294

European-Non Finnish (NFE)

AF:

0.819

AC:

55711

AN:

68000

Other (OTH)

AF:

0.862

AC:

1822

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

977

1955

2932

3910

4887

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

884

1768

2652

3536

4420

<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:

0.836

Hom.:

155052

Bravo

AF:

0.865

Asia WGS

AF:

0.783

AC:

2722

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

6.1

(source)

DANN

Benign

0.20

PhyloP100

-0.88

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