Variant 10-118113229-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000435944.5(CASC2):n.452+61033G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00729 in 152,166 control chromosomes in the GnomAD database, including 16 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 0.0073 ( 16 hom., cov: 32)

Consequence

CASC2
ENST00000435944.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.679

Variant links:

Genes affected

CASC2 (HGNC:):

CASC2 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=-0.91).

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00729 (1109/152166) while in subpopulation AFR AF= 0.0254 (1056/41508). AF 95% confidence interval is 0.0242. There are 16 homozygotes in gnomad4. There are 509 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 16 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC2	NR_026939.1 linkuse as main transcript	n.455+61033G>A		intron_variant
CASC2	NR_026940.1 linkuse as main transcript	n.455+61033G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CASC2	ENST00000435944.5 linkuse as main transcript	n.452+61033G>A	intron_variant	1
CASC2	ENST00000414722.5 linkuse as main transcript	n.541+61033G>A	intron_variant	5
CASC2	ENST00000439517.2 linkuse as main transcript	n.154+63612G>A	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.00721

AC:

1097

AN:

152048

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0252

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00236

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000208

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0000735

Gnomad OTH

AF:

0.00478

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

GnomAD4 genome

AF:

0.00729

AC:

1109

AN:

152166

Hom.:

Cov.:

AF XY:

0.00684

AC XY:

509

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.0254

Gnomad4 AMR

AF:

0.00236

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000208

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000735

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00555

Hom.:

Bravo

AF:

0.00842

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.7

DANN

Benign

0.56

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