chr16-52629949-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000261261 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564331.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261261	ENST00000564331.1	TSL:3	n.94G>A		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000261261	ENST00000659170.1		n.488G>A		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000261261	ENST00000666586.1		n.482G>A		non_coding_transcript_exon	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

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) AF: 0.500 AC: 3 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.302 AC: 12495 AN: 41316

American (AMR) AF: 0.235 AC: 3577 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3468

East Asian (EAS) AF: 0.257 AC: 1321 AN: 5146

South Asian (SAS) AF: 0.224 AC: 1072 AN: 4796

European-Finnish (FIN) AF: 0.207 AC: 2171 AN: 10484

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17156 AN: 67918

Other (OTH) AF: 0.285 AC: 599 AN: 2104

Alfa AF: 0.252 Hom.: 638

Bravo AF: 0.267

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	15
DANN	Benign	0.76
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs9940048; hg19: chr16-52663861;