rs1891086

Variant names:

• chr6-22221900-A-C
• rs1891086
• ENST00000567753.2:n.1792A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-22221900-A-C
• chr6-22221900-A-G
• chr6-22221900-A-T

Variant summary

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

The ENST00000567753.2(CASC15):​n.1792A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,014 control chromosomes in the GnomAD database, including 37,448 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 0.70 (37448 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: CASC15 ENST00000567753.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635
• Publications: 3 publications found

Genes affected

CASC15 (HGNC:28245): (cancer susceptibility 15) This gene produces a long non-coding RNA that may regulate cell proliferation. This RNA is upregulated in hepatocellular carcinoma, where it is thought to function as an oncogene. However, some splice variants of this gene may function as a tumor suppressor in neuroblastoma and other tumor types. Circular RNA variants were observed at this gene. [provided by RefSeq, Dec 2017]

NBAT1 (HGNC:49075): (neuroblastoma associated transcript 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.739 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
CASC15	ENST00000567753.2	n.1792A>C		non_coding_transcript_exon_variant	Exon 3 of 3	6
CASC15	ENST00000636388.1	n.617A>C		non_coding_transcript_exon_variant	Exon 3 of 3	5
CASC15	ENST00000653763.1	n.673A>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106390 AN: 151894 Hom.: 37427 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.690

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.700 AC: 106460 AN: 152012 Hom.: 37448 Cov.: 31 AF XY: 0.697 AC XY: 51818 AN XY: 74292

African (AFR) AF: 0.662 AC: 27408 AN: 41424

American (AMR) AF: 0.635 AC: 9696 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2447 AN: 3472

East Asian (EAS) AF: 0.684 AC: 3533 AN: 5164

South Asian (SAS) AF: 0.548 AC: 2644 AN: 4822

European-Finnish (FIN) AF: 0.748 AC: 7904 AN: 10564

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50582 AN: 67984

Other (OTH) AF: 0.691 AC: 1456 AN: 2106

Alfa AF: 0.726 Hom.: 60663

Bravo AF: 0.691

Asia WGS AF: 0.611 AC: 2129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.7
DANN	Benign	0.82
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs1891086; hg19: chr6-22222129;