rs6994721

Variant names:

• chr8-75145478-A-G
• rs6994721
• ENST00000676364.2:n.251-23722T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-75145478-A-G
• chr8-75145478-A-T

Variant summary

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

The ENST00000676364.2(CASC9):​n.251-23722T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,766 control chromosomes in the GnomAD database, including 18,776 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 0.49 (18776 hom., cov: 32)
• Consequence: CASC9 ENST00000676364.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 4 publications found

Genes affected

CASC9 (HGNC:48906): (cancer susceptibility 9)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000676364.2. 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
	CASC9	ENST00000676364.2		n.251-23722T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73677 AN: 151646 Hom.: 18750 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.391

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.486 AC: 73752 AN: 151766 Hom.: 18776 Cov.: 32 AF XY: 0.486 AC XY: 36011 AN XY: 74130

African (AFR) AF: 0.651 AC: 27001 AN: 41446

American (AMR) AF: 0.496 AC: 7538 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3466

East Asian (EAS) AF: 0.338 AC: 1742 AN: 5152

South Asian (SAS) AF: 0.380 AC: 1825 AN: 4808

European-Finnish (FIN) AF: 0.483 AC: 5074 AN: 10508

Middle Eastern (MID) AF: 0.400 AC: 116 AN: 290

European-Non Finnish (NFE) AF: 0.409 AC: 27763 AN: 67870

Other (OTH) AF: 0.471 AC: 993 AN: 2110

Alfa AF: 0.428 Hom.: 44258

Bravo AF: 0.497

Asia WGS AF: 0.395 AC: 1371 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.51
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6994721; hg19: chr8-76057713;