dbSNP rs582970: ENSG00000285681:n.215+17554T>C (chr18-60497226-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 ENST00000650201.1(ENSG00000285681):n.215+17554T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,004 control chromosomes in the GnomAD database, including 14,099 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 0.43 ( 14099 hom., cov: 32)

Consequence

ENSG00000285681
ENST00000650201.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0420

Publications

5 publications found

Variant links:

Genes affected

ENSG00000285681 (HGNC:):

ENSG00000285681 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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000285681	ENST00000650201.1 link	n.215+17554T>C	intron_variant	Intron 2 of 3
ENSG00000285681	ENST00000658928.1 link	n.258+17554T>C	intron_variant	Intron 2 of 3
ENSG00000285681	ENST00000667405.1 link	n.128+17554T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.425

AC:

64611

AN:

151886

Hom.:

14077

Cov.:

show subpopulations

Gnomad AFR

AF:

0.516

Gnomad AMI

AF:

0.332

Gnomad AMR

AF:

0.350

Gnomad ASJ

AF:

0.451

Gnomad EAS

AF:

0.346

Gnomad SAS

AF:

0.475

Gnomad FIN

AF:

0.449

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.387

Gnomad OTH

AF:

0.400

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

GnomAD4 genome

AF:

0.425

AC:

64676

AN:

152004

Hom.:

14099

Cov.:

AF XY:

0.425

AC XY:

31587

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.517

AC:

21420

AN:

41444

American (AMR)

AF:

0.350

AC:

5346

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.451

AC:

1566

AN:

3472

East Asian (EAS)

AF:

0.346

AC:

1795

AN:

5184

South Asian (SAS)

AF:

0.473

AC:

2281

AN:

4820

European-Finnish (FIN)

AF:

0.449

AC:

4721

AN:

10522

Middle Eastern (MID)

AF:

0.425

AC:

124

AN:

292

European-Non Finnish (NFE)

AF:

0.387

AC:

26280

AN:

67952

Other (OTH)

AF:

0.398

AC:

841

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1900

3799

5699

7598

9498

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

610

1220

1830

2440

3050

<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:

0.308

Hom.:

947

Bravo

AF:

0.420

Asia WGS

AF:

0.412

AC:

1431

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

4.1

(source)

DANN

Benign

0.73

PhyloP100

0.042

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