rs9939524

chr16-57689840-A-G

Variant summary

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

The ENST00000563062.1(ENSG00000260467):n.464-3020T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 456,426 control chromosomes in the GnomAD database, including 11,337 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 0.22 (4844 hom., cov: 32)
  • Exomes 𝑓: 0.19 (6493 hom.)
• Consequence: ENST00000563062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000563062.1	n.464-3020T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34084 AN: 151940 Hom.: 4826 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.202

GnomAD3 exomes AF: 0.211 AC: 28842 AN: 136984 Hom.: 3784 AF XY: 0.207 AC XY: 15424 AN XY: 74482

Gnomad AFR exome AF: 0.381

Gnomad AMR exome AF: 0.326

Gnomad ASJ exome AF: 0.0971

Gnomad EAS exome AF: 0.328

Gnomad SAS exome AF: 0.243

Gnomad FIN exome AF: 0.107

Gnomad NFE exome AF: 0.135

Gnomad OTH exome AF: 0.170

GnomAD4 exome AF: 0.186 AC: 56560 AN: 304368 Hom.: 6493 Cov.: 0 AF XY: 0.190 AC XY: 32848 AN XY: 173318

Gnomad4 AFR exome AF: 0.373

Gnomad4 AMR exome AF: 0.324

Gnomad4 ASJ exome AF: 0.0962

Gnomad4 EAS exome AF: 0.338

Gnomad4 SAS exome AF: 0.249

Gnomad4 FIN exome AF: 0.113

Gnomad4 NFE exome AF: 0.133

Gnomad4 OTH exome AF: 0.175

GnomAD4 genome AF: 0.225 AC: 34151 AN: 152058 Hom.: 4844 Cov.: 32 AF XY: 0.227 AC XY: 16899 AN XY: 74330

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.0850

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.205

Alfa AF: 0.153 Hom.: 2618

Bravo AF: 0.246

Asia WGS AF: 0.271 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	6.3
Dann	Uncertain	0.99

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9939524; hg19: chr16-57723752; COSMIC: COSV59653478;