rs16967753

Variant names:

• chr16-64601500-C-T
• rs16967753
• ENST00000808892.1:n.535+1244C>T

Variant summary

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

The ENST00000808892.1(ENSG00000259846):​n.535+1244C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0376 in 151,856 control chromosomes in the GnomAD database, including 278 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 0.038 (278 hom., cov: 32)
• Consequence: ENSG00000259846 ENST00000808892.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 0 publications found

Genes affected

ENSG00000259846 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808892.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259846	ENST00000808892.1		n.535+1244C>T		intron	N/A
	ENSG00000259846	ENST00000808893.1		n.521+1244C>T		intron	N/A
	ENSG00000259846	ENST00000808894.1		n.643+1244C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0376 AC: 5700 AN: 151738 Hom.: 278 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0151

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.0933

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00379

Gnomad OTH AF: 0.0293

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

GnomAD4 genome AF: 0.0376 AC: 5704 AN: 151856 Hom.: 278 Cov.: 32 AF XY: 0.0387 AC XY: 2875 AN XY: 74230

African (AFR) AF: 0.112 AC: 4644 AN: 41442

American (AMR) AF: 0.0150 AC: 228 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3464

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5128

South Asian (SAS) AF: 0.0932 AC: 450 AN: 4830

European-Finnish (FIN) AF: 0.000471 AC: 5 AN: 10612

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00379 AC: 257 AN: 67866

Other (OTH) AF: 0.0290 AC: 61 AN: 2106

Alfa AF: 0.0195 Hom.: 67

Bravo AF: 0.0398

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.61
DANN	Benign	0.75
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs16967753; hg19: chr16-64635403;