chr6-91582200-T-A

Variant names:

• chr6-91582200-T-A
• rs3857501
• ENST00000656997.1:n.718-22542A>T

Variant summary

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

The ENST00000656997.1(CASC6):​n.718-22542A>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.729 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC6	ENST00000656997.1		n.718-22542A>T		intron	N/A
	CASC6	ENST00000760409.1		n.565-22542A>T		intron	N/A
	CASC6	ENST00000760410.1		n.389-20631A>T		intron	N/A

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

African (AFR) AF: 0.421 AC: 17429 AN: 41410

American (AMR) AF: 0.740 AC: 11275 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2462 AN: 3468

East Asian (EAS) AF: 0.431 AC: 2201 AN: 5106

South Asian (SAS) AF: 0.655 AC: 3159 AN: 4820

European-Finnish (FIN) AF: 0.655 AC: 6928 AN: 10584

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45376 AN: 67888

Other (OTH) AF: 0.608 AC: 1283 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.44
PhyloP100		-1.2

Splicing

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

Other links and lift over

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