dbSNP rs1224606: ENSG00000259754:n.188+40705T>C (chr15-47853621-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 ENST00000662551.1(ENSG00000259754):n.188+40705T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,144 control chromosomes in the GnomAD database, including 4,269 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 0.16 ( 4269 hom., cov: 33)

Consequence

ENSG00000259754
ENST00000662551.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Publications

0 publications found

Variant links:

Genes affected

ENSG00000259754 (HGNC:):

ENSG00000259754 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000259754	ENST00000662551.1 link	n.188+40705T>C	intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1 link	n.188+40705T>C	intron_variant	Intron 1 of 5
ENSG00000259754	ENST00000665188.1 link	n.68+40705T>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24711

AN:

152024

Hom.:

4252

Cov.:

show subpopulations

Gnomad AFR

AF:

0.443

Gnomad AMI

AF:

0.0746

Gnomad AMR

AF:

0.0944

Gnomad ASJ

AF:

0.0303

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.0622

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0387

Gnomad OTH

AF:

0.115

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

GnomAD4 genome

AF:

0.163

AC:

24778

AN:

152144

Hom.:

4269

Cov.:

AF XY:

0.159

AC XY:

11860

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.443

AC:

18371

AN:

41440

American (AMR)

AF:

0.0950

AC:

1452

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0303

AC:

105

AN:

3466

East Asian (EAS)

AF:

0.123

AC:

635

AN:

5180

South Asian (SAS)

AF:

0.122

AC:

589

AN:

4828

European-Finnish (FIN)

AF:

0.0622

AC:

660

AN:

10606

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0387

AC:

2633

AN:

68020

Other (OTH)

AF:

0.117

AC:

247

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

826

1652

2478

3304

4130

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

238

476

714

952

1190

<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:

0.0823

Hom.:

1965

Bravo

AF:

0.176

Asia WGS

AF:

0.148

AC:

515

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.5

(source)

DANN

Benign

0.75

PhyloP100

1.1

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