rs9940048

Variant names:

• chr16-52629949-G-A
• rs9940048
• ENST00000564331.1:n.94G>A

Variant summary

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

The ENST00000564331.1(ENSG00000261261):​n.94G>A 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 0.263 in 151,678 control chromosomes in the GnomAD database, including 5,409 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 0.26 (5409 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000261261 ENST00000564331.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566

Genes affected

ENSG00000261261 (HGNC:):

CASC16 (HGNC:48608): (cancer susceptibility 16)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 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
ENSG00000261261	ENST00000564331.1	n.94G>A		non_coding_transcript_exon_variant	Exon 2 of 4	3
ENSG00000261261	ENST00000659170.1	n.488G>A		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000261261	ENST00000666586.1	n.482G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39925 AN: 151556 Hom.: 5406 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.287

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.263 AC: 39944 AN: 151672 Hom.: 5409 Cov.: 32 AF XY: 0.259 AC XY: 19175 AN XY: 74098

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.285

Alfa AF: 0.263 Hom.: 488

Bravo AF: 0.267

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	15
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9940048; hg19: chr16-52663861;