chr8-127705823-G-T

Variant names:

• chr8-127705823-G-T
• rs9642880
• ENST00000502463.7:n.144-13957C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000502463.7(CASC11):​n.144-13957C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,044 control chromosomes in the GnomAD database, including 23,875 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 0.54 (23875 hom., cov: 32)
• Consequence: CASC11 ENST00000502463.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695
• Publications: 120 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502463.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC11	NR_117102.1		n.366-2580C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC11	ENST00000502463.7	TSL:2	n.144-13957C>A		intron	N/A
	CASC11	ENST00000519071.6	TSL:3	n.355-2580C>A		intron	N/A
	CASC11	ENST00000672637.1		n.272-2580C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82481 AN: 151926 Hom.: 23840 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.543 AC: 82571 AN: 152044 Hom.: 23875 Cov.: 32 AF XY: 0.544 AC XY: 40459 AN XY: 74312

African (AFR) AF: 0.757 AC: 31394 AN: 41464

American (AMR) AF: 0.462 AC: 7057 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1671 AN: 3470

East Asian (EAS) AF: 0.326 AC: 1684 AN: 5172

South Asian (SAS) AF: 0.556 AC: 2677 AN: 4818

European-Finnish (FIN) AF: 0.529 AC: 5576 AN: 10550

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30995 AN: 67980

Other (OTH) AF: 0.505 AC: 1064 AN: 2106

Alfa AF: 0.475 Hom.: 83920

Bravo AF: 0.543

Asia WGS AF: 0.501 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.94
DANN	Benign	0.63
PhyloP100		-0.69

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9642880;

hg19: chr8-128718068;