8-127734306-T-C

Variant names:

• chr8-127734306-T-C
• rs146032527
• ENST00000672942.1:n.195-347A>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The ENST00000672942.1(CASC11):​n.195-347A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 152,330 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.010 (19 hom., cov: 32)
• Consequence: CASC11 ENST00000672942.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.351

Genes affected

CASC11 (HGNC:48939): (cancer susceptibility 11)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 8-127734306-T-C is Benign according to our data. Variant chr8-127734306-T-C is described in ClinVar as [Benign]. Clinvar id is 2658809.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 19 gene

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
CASC11	ENST00000672942.1	n.195-347A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0102 AC: 1549 AN: 152212 Hom.: 19 Cov.: 32

Gnomad AFR AF: 0.00241

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.00373

Gnomad ASJ AF: 0.00894

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.0319

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0144

Gnomad OTH AF: 0.00764

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

GnomAD4 genome AF: 0.0102 AC: 1549 AN: 152330 Hom.: 19 Cov.: 32 AF XY: 0.0110 AC XY: 817 AN XY: 74490

Gnomad4 AFR AF: 0.00241

Gnomad4 AMR AF: 0.00372

Gnomad4 ASJ AF: 0.00894

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00269

Gnomad4 FIN AF: 0.0319

Gnomad4 NFE AF: 0.0144

Gnomad4 OTH AF: 0.00756

Alfa AF: 0.0121 Hom.: 4

Bravo AF: 0.00780

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jan 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CASC11: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs146032527; hg19: chr8-128746552;