6-91604261-T-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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
CASC6	ENST00000656997.1	n.717+19838A>C		intron_variant	Intron 2 of 3

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

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.334

Alfa AF: 0.359 Hom.: 20289

Bravo AF: 0.362

Asia WGS AF: 0.526 AC: 1825 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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