rs9466269

chr6-22136180-T-C

Variant summary

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

The NR_034143.1(NBAT1):n.717A>G 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 0.417 in 152,756 control chromosomes in the GnomAD database, including 13,862 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 0.42 (13840 hom., cov: 32)
  • Exomes 𝑓: 0.21 (22 hom.)
• Consequence: NBAT1 NR_034143.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709

Genes affected

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

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NBAT1	NR_034143.1	n.717A>G		non_coding_transcript_exon_variant	3/3
CASC15	NR_015410.2	n.1422+25260T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NBAT1	ENST00000566912.2	n.717A>G		non_coding_transcript_exon_variant	3/3	2
CASC15	ENST00000688254.1	n.1152-78127T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63550 AN: 151944 Hom.: 13832 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.403

GnomAD4 exome AF: 0.212 AC: 147 AN: 694 Hom.: 22 Cov.: 0 AF XY: 0.194 AC XY: 74 AN XY: 382

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.160

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.0789

Gnomad4 SAS exome AF: 0.222

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.221

Gnomad4 OTH exome AF: 0.233

GnomAD4 genome AF: 0.418 AC: 63584 AN: 152062 Hom.: 13840 Cov.: 32 AF XY: 0.419 AC XY: 31140 AN XY: 74366

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.401

Alfa AF: 0.382 Hom.: 23284

Bravo AF: 0.411

Asia WGS AF: 0.361 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	5.8
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9466269; hg19: chr6-22136409;