16-85942053-C-T

Variant names:

• chr16-85942053-C-T
• rs305061
• ENST00000645383.1:n.394-3363C>T

Variant summary

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

The ENST00000645383.1(ENSG00000285163):​n.394-3363C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,184 control chromosomes in the GnomAD database, including 41,771 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 0.73 (41771 hom., cov: 33)
• Consequence: ENSG00000285163 ENST00000645383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 33 publications found

Genes affected

ENSG00000285163 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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
ENSG00000285163	ENST00000645383.1	n.394-3363C>T		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646214.1	n.78-3363C>T		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646986.2	n.716-3363C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111712 AN: 152064 Hom.: 41712 Cov.: 33

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.735 AC: 111838 AN: 152184 Hom.: 41771 Cov.: 33 AF XY: 0.741 AC XY: 55105 AN XY: 74400

African (AFR) AF: 0.842 AC: 34941 AN: 41522

American (AMR) AF: 0.749 AC: 11457 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2151 AN: 3470

East Asian (EAS) AF: 0.863 AC: 4479 AN: 5188

South Asian (SAS) AF: 0.763 AC: 3680 AN: 4820

European-Finnish (FIN) AF: 0.773 AC: 8183 AN: 10580

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44767 AN: 67998

Other (OTH) AF: 0.697 AC: 1470 AN: 2110

Alfa AF: 0.682 Hom.: 168413

Bravo AF: 0.738

Asia WGS AF: 0.823 AC: 2860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.67
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs305061; hg19: chr16-85975659;