ENST00000566770.1:n.126-2381T>C

Variant names:

• chr16-50109033-A-G
• rs8046148
• ENST00000566770.1:n.126-2381T>C

Variant summary

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

The ENST00000566770.1(ENSG00000260381):​n.126-2381T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 151,558 control chromosomes in the GnomAD database, including 44,671 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 0.77 (44671 hom., cov: 30)
• Consequence: ENSG00000260381 ENST00000566770.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.37

Genes affected

ENSG00000260381 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.812 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
ENSG00000260381	ENST00000566770.1	n.126-2381T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116073 AN: 151438 Hom.: 44634 Cov.: 30

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.767 AC: 116170 AN: 151558 Hom.: 44671 Cov.: 30 AF XY: 0.769 AC XY: 56893 AN XY: 73976

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.759

Alfa AF: 0.780 Hom.: 84015

Bravo AF: 0.752

Asia WGS AF: 0.753 AC: 2621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8046148; hg19: chr16-50142944;