chr16-57689840-A-G

Variant names:

• chr16-57689840-A-G
• rs9939524
• ENST00000563062.1:n.464-3020T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000563062.1(ENSG00000260467):​n.464-3020T>C variant causes a intron 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: ENSG00000260467 ENST00000563062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453
• Publications: 3 publications found

Genes affected

ENSG00000260467 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563062.1. 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
	ENSG00000260467	ENST00000563062.1	TSL:5	n.464-3020T>C		intron	N/A

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

GnomAD2 exomes AF: 0.211 AC: 28842 AN: 136984 AF XY: 0.207

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 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

African (AFR) AF: 0.373 AC: 3215 AN: 8628

American (AMR) AF: 0.324 AC: 8843 AN: 27280

Ashkenazi Jewish (ASJ) AF: 0.0962 AC: 1038 AN: 10788

East Asian (EAS) AF: 0.338 AC: 3112 AN: 9210

South Asian (SAS) AF: 0.249 AC: 14875 AN: 59744

European-Finnish (FIN) AF: 0.113 AC: 1442 AN: 12784

Middle Eastern (MID) AF: 0.162 AC: 451 AN: 2782

European-Non Finnish (NFE) AF: 0.133 AC: 21085 AN: 158912

Other (OTH) AF: 0.175 AC: 2499 AN: 14240

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

African (AFR) AF: 0.379 AC: 15729 AN: 41470

American (AMR) AF: 0.286 AC: 4379 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0850 AC: 295 AN: 3470

East Asian (EAS) AF: 0.328 AC: 1685 AN: 5136

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4812

European-Finnish (FIN) AF: 0.102 AC: 1082 AN: 10598

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9208 AN: 67968

Other (OTH) AF: 0.205 AC: 434 AN: 2112

Alfa AF: 0.175 Hom.: 5467

Bravo AF: 0.246

Asia WGS AF: 0.271 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.3
DANN	Uncertain	0.99
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

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