dbSNP rs10978781: ENSG00000224848:n.270-27262T>C (chr9-96746198-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000653137.3(ENSG00000224848):n.270-27262T>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
ENST00000653137.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.889

Variant links:

Genes affected

ENSG00000224848 (HGNC:):

ENSG00000224848 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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	ENST00000653137.3 link	n.270-27262T>C	intron_variant	Intron 1 of 1
ENSG00000224848	ENST00000656729.2 link	n.256+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

Gnomad4 AFR

AF:

0.635

Gnomad4 AMR

AF:

0.0927

Gnomad4 ASJ

AF:

0.0251

Gnomad4 EAS

AF:

0.348

Gnomad4 SAS

AF:

0.118

Gnomad4 FIN

AF:

0.0927

Gnomad4 NFE

AF:

0.0168

Gnomad4 OTH

AF:

0.152

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

DANN

Benign

0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over