Genetic Variant ENSG00000232855:n.1562-61A>C (chr21-28417219-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000657148.1(ENSG00000232855):n.1562-61A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.077 ( 223 hom., cov: 0)

Consequence

ENSG00000232855
ENST00000657148.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.81

Publications

1 publications found

Variant links:

Genes affected

ENSG00000232855 (HGNC:58104):

ENSG00000232855 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 (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000232855	ENST00000657148.1 link	n.1562-61A>C	intron_variant	Intron 3 of 4
ENSG00000232855	ENST00000824757.1 link	n.686-61A>C	intron_variant	Intron 5 of 8
ENSG00000232855	ENST00000824758.1 link	n.1097-61A>C	intron_variant	Intron 8 of 11
ENSG00000232855	ENST00000824759.1 link	n.768-61A>C	intron_variant	Intron 5 of 8

Frequencies

GnomAD3 genomes

AF:

0.0769

AC:

4325

AN:

56234

Hom.:

224

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0358

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00278

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000665

Gnomad OTH

AF:

0.0648

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

GnomAD4 genome

AF:

0.0769

AC:

4325

AN:

56264

Hom.:

223

Cov.:

AF XY:

0.0724

AC XY:

1946

AN XY:

26886

show subpopulations

African (AFR)

AF:

0.205

AC:

4096

AN:

19988

American (AMR)

AF:

0.0358

AC:

169

AN:

4724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1040

East Asian (EAS)

AF:

0.00

AC:

AN:

3072

South Asian (SAS)

AF:

0.00140

AC:

AN:

1432

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2426

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.000665

AC:

AN:

22548

Other (OTH)

AF:

0.0640

AC:

AN:

672

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.528

Heterozygous variant carriers

176

351

527

702

878

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

168

210

<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:

0.0162

Hom.:

Bravo

AF:

0.0339

Asia WGS

AF:

0.00463

AC:

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.14

(source)

DANN

Benign

0.61

PhyloP100

-1.8

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