Variant rs1153303 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000467409.6(ABCC13):n.379-2160T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,204 control chromosomes in the GnomAD database, including 52,235 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 0.82 ( 52235 hom., cov: 34)

Consequence

ABCC13
ENST00000467409.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.42

Variant links:

Genes affected

ABCC13 (HGNC:):

ABCC13 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.35).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCC13	NR_003087.1 linkuse as main transcript	n.422-2160T>G		intron_variant
ABCC13	NR_003088.1 linkuse as main transcript	n.422-2160T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ABCC13	ENST00000467409.6 linkuse as main transcript	n.379-2160T>G	intron_variant	1
ABCC13	ENST00000471902.5 linkuse as main transcript	n.285-2160T>G	intron_variant	1
ABCC13	ENST00000481582.5 linkuse as main transcript	n.341-2160T>G	intron_variant	1

Frequencies

GnomAD3 genomes

AF:

0.825

AC:

125418

AN:

152086

Hom.:

52186

Cov.:

show subpopulations

Gnomad AFR

AF:

0.928

Gnomad AMI

AF:

0.845

Gnomad AMR

AF:

0.704

Gnomad ASJ

AF:

0.903

Gnomad EAS

AF:

0.673

Gnomad SAS

AF:

0.772

Gnomad FIN

AF:

0.789

Gnomad MID

AF:

0.930

Gnomad NFE

AF:

0.805

Gnomad OTH

AF:

0.830

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

GnomAD4 genome

AF:

0.825

AC:

125517

AN:

152204

Hom.:

52235

Cov.:

AF XY:

0.820

AC XY:

60982

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.928

Gnomad4 AMR

AF:

0.703

Gnomad4 ASJ

AF:

0.903

Gnomad4 EAS

AF:

0.673

Gnomad4 SAS

AF:

0.772

Gnomad4 FIN

AF:

0.789

Gnomad4 NFE

AF:

0.805

Gnomad4 OTH

AF:

0.830

Alfa

AF:

0.808

Hom.:

97142

Bravo

AF:

0.822

Asia WGS

AF:

0.747

AC:

2599

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.35

CADD

Benign

DANN

Benign

0.74

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