rs3857501

chr6-91582200-T-Achr6-91582200-T-Cchr6-91582200-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656997.1(CASC6):n.718-22542A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,824 control chromosomes in the GnomAD database, including 28,474 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 0.60 (28474 hom., cov: 31)
• Consequence: CASC6 ENST00000656997.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC6	ENST00000656997.1	n.718-22542A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90917 AN: 151706 Hom.: 28455 Cov.: 31

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.599 AC: 90973 AN: 151824 Hom.: 28474 Cov.: 31 AF XY: 0.600 AC XY: 44476 AN XY: 74178

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.608

Alfa AF: 0.517 Hom.: 1534

Bravo AF: 0.597

Asia WGS AF: 0.572 AC: 1990 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.37
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3857501; hg19: chr6-92291918; COSMIC: COSV70045980;