ENST00000569778.1:n.60+578G>T

Variant names:

• chr16-56610738-C-A
• rs1580833
• ENST00000569778.1:n.60+578G>T

Variant summary

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

The ENST00000569778.1(ENSG00000260823):​n.60+578G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,030 control chromosomes in the GnomAD database, including 8,558 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 0.32 (8558 hom., cov: 32)
• Consequence: ENSG00000260823 ENST00000569778.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563
• Publications: 18 publications found

Genes affected

ENSG00000260823 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000569778.1. 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
	ENSG00000260823	ENST00000569778.1	TSL:2	n.60+578G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49165 AN: 151912 Hom.: 8542 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.333

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.324 AC: 49212 AN: 152030 Hom.: 8558 Cov.: 32 AF XY: 0.328 AC XY: 24396 AN XY: 74314

African (AFR) AF: 0.324 AC: 13416 AN: 41416

American (AMR) AF: 0.330 AC: 5047 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3468

East Asian (EAS) AF: 0.713 AC: 3687 AN: 5172

South Asian (SAS) AF: 0.412 AC: 1987 AN: 4824

European-Finnish (FIN) AF: 0.237 AC: 2514 AN: 10590

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20299 AN: 67964

Other (OTH) AF: 0.336 AC: 709 AN: 2108

Alfa AF: 0.312 Hom.: 1049

Bravo AF: 0.335

Asia WGS AF: 0.520 AC: 1807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1580833; hg19: chr16-56644650;