rs8046148

Positions:

• chr16-50109033-A-G
• chr16-50109033-A-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000260381	ENST00000566770.1	n.126-2381T>C		intron_variant		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;