dbSNP rs889206: ENSG00000260242:n.48+49078G>A (chr16-18123938-C-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000563866.1(ENSG00000260242):n.48+49078G>A 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 0.0016 ( 0 hom., cov: 17)

Failed GnomAD Quality Control

Consequence

ENSG00000260242
ENST00000563866.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0150

Publications

1 publications found

Variant links:

Genes affected

ENSG00000260242 (HGNC:):

ENSG00000260242 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260242	ENST00000563866.1 link	n.48+49078G>A		intron_variant	Intron 1 of 1	3
ENSG00000259929	ENST00000567304.1 link	n.144+27514G>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.00164

AC:

182

AN:

110868

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00109

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00140

Gnomad ASJ

AF:

0.000826

Gnomad EAS

AF:

0.00385

Gnomad SAS

AF:

0.00269

Gnomad FIN

AF:

0.000836

Gnomad MID

AF:

0.0250

Gnomad NFE

AF:

0.00192

Gnomad OTH

AF:

0.00141

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00165

AC:

183

AN:

110984

Hom.:

Cov.:

AF XY:

0.00146

AC XY:

AN XY:

54274

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00112

AC:

AN:

31244

American (AMR)

AF:

0.00139

AC:

AN:

10044

Ashkenazi Jewish (ASJ)

AF:

0.000826

AC:

AN:

2420

East Asian (EAS)

AF:

0.00385

AC:

AN:

3632

South Asian (SAS)

AF:

0.00268

AC:

AN:

2980

European-Finnish (FIN)

AF:

0.000836

AC:

AN:

8374

Middle Eastern (MID)

AF:

0.0263

AC:

AN:

190

European-Non Finnish (NFE)

AF:

0.00192

AC:

AN:

49990

Other (OTH)

AF:

0.00139

AC:

AN:

1434

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.251

Heterozygous variant carriers

101

126

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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

Alfa

AF:

0.0483

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.1

(source)

DANN

Benign

0.44

PhyloP100

0.015

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