dbSNP rs10978781: ENSG00000224848:n.286-27262T>C (chr9-96746198-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 ENST00000653137.4(ENSG00000224848):n.286-27262T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,134 control chromosomes in the GnomAD database, including 8,976 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 0.21 ( 8976 hom., cov: 32)

Consequence

ENSG00000224848
ENST00000653137.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.889

Publications

5 publications found

Variant links:

Genes affected

ENSG00000224848 (HGNC:):

ENSG00000224848 links:

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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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000224848	ENST00000653137.4 link	n.286-27262T>C	intron_variant	Intron 1 of 1
ENSG00000224848	ENST00000656729.3 link	n.272+25068T>C	intron_variant	Intron 2 of 2
ENSG00000224848	ENST00000661289.3 link	n.472+25068T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.214

AC:

32583

AN:

152016

Hom.:

8926

Cov.:

show subpopulations

Gnomad AFR

AF:

0.634

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.0929

Gnomad ASJ

AF:

0.0251

Gnomad EAS

AF:

0.348

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.0927

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0169

Gnomad OTH

AF:

0.153

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

GnomAD4 genome

AF:

0.215

AC:

32679

AN:

152134

Hom.:

8976

Cov.:

AF XY:

0.216

AC XY:

16037

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.635

AC:

26325

AN:

41460

American (AMR)

AF:

0.0927

AC:

1418

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0251

AC:

AN:

3472

East Asian (EAS)

AF:

0.348

AC:

1795

AN:

5160

South Asian (SAS)

AF:

0.118

AC:

568

AN:

4824

European-Finnish (FIN)

AF:

0.0927

AC:

982

AN:

10594

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0168

AC:

1145

AN:

68004

Other (OTH)

AF:

0.152

AC:

320

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

728

1457

2185

2914

3642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

264

528

792

1056

1320

<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:

0.145

Hom.:

1374

Bravo

AF:

0.235

Asia WGS

AF:

0.209

AC:

727

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.7

(source)

DANN

Benign

0.68

PhyloP100

-0.89

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