ENST00000656997.1:n.717+19838A>C

Variant names:

• chr6-91604261-T-G
• rs9353859
• ENST00000656997.1:n.717+19838A>C

Variant summary

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

The ENST00000656997.1(CASC6):​n.717+19838A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,082 control chromosomes in the GnomAD database, including 10,784 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 0.36 (10784 hom., cov: 33)
• Consequence: CASC6 ENST00000656997.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 2 publications found

Genes affected

CASC6 (HGNC:49076): (cancer susceptibility 6)

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 (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656997.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC6	ENST00000656997.1		n.717+19838A>C		intron	N/A
	CASC6	ENST00000760409.1		n.564+19838A>C		intron	N/A
	CASC6	ENST00000760410.1		n.388+19838A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55433 AN: 151964 Hom.: 10786 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.365 AC: 55438 AN: 152082 Hom.: 10784 Cov.: 33 AF XY: 0.376 AC XY: 27965 AN XY: 74334

African (AFR) AF: 0.283 AC: 11753 AN: 41486

American (AMR) AF: 0.439 AC: 6705 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1021 AN: 3472

East Asian (EAS) AF: 0.706 AC: 3628 AN: 5142

South Asian (SAS) AF: 0.486 AC: 2343 AN: 4824

European-Finnish (FIN) AF: 0.450 AC: 4770 AN: 10596

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24197 AN: 67974

Other (OTH) AF: 0.334 AC: 706 AN: 2114

Alfa AF: 0.360 Hom.: 42935

Bravo AF: 0.362

Asia WGS AF: 0.526 AC: 1825 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.97
DANN	Benign	0.60
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs9353859; hg19: chr6-92313979; COSMIC: COSV60245798;