rs9466269

Positions:

• chr6-22136180-T-C

Variant summary

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

The ENST00000566912.2(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 ENST00000566912.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709

Genes affected

CASC15 (HGNC:):

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	Protein	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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000444265.6	n.1061+25260T>C		intron_variant		1
NBAT1	ENST00000566912.2	n.717A>G		non_coding_transcript_exon_variant	3/3	2
CASC15	ENST00000606851.5	n.1391+25260T>C		intron_variant		2

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;