rs12547643

Variant names:

• chr8-127700928-G-A
• rs12547643
• ENST00000502463.7:n.144-9062C>T

Variant summary

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

The ENST00000502463.7(CASC11):​n.144-9062C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,052 control chromosomes in the GnomAD database, including 6,359 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 0.27 (6359 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: CASC11 ENST00000502463.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 13 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 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.560-89C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC11	ENST00000502463.7	TSL:2	n.144-9062C>T		intron	N/A
	CASC11	ENST00000519071.6	TSL:3	n.549-89C>T		intron	N/A
	CASC11	ENST00000672637.1		n.466-1369C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40658 AN: 151930 Hom.: 6347 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.274

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.268 AC: 40691 AN: 152048 Hom.: 6359 Cov.: 32 AF XY: 0.271 AC XY: 20121 AN XY: 74312

African (AFR) AF: 0.121 AC: 5012 AN: 41486

American (AMR) AF: 0.197 AC: 3011 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1496 AN: 3470

East Asian (EAS) AF: 0.170 AC: 877 AN: 5174

South Asian (SAS) AF: 0.453 AC: 2182 AN: 4816

European-Finnish (FIN) AF: 0.365 AC: 3844 AN: 10538

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23310 AN: 67968

Other (OTH) AF: 0.283 AC: 598 AN: 2110

Alfa AF: 0.323 Hom.: 16484

Bravo AF: 0.242

Asia WGS AF: 0.282 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.36
PhyloP100		-1.2

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: rs12547643;

hg19: chr8-128713173;