16-49319593-A-T

Variant names:

• chr16-49319593-A-T
• rs2216263
• ENST00000564048.2:n.136-10874A>T

Variant summary

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

The ENST00000643467.1(SYNAGE):​n.659-10874A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 151,268 control chromosomes in the GnomAD database, including 38,225 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 0.69 (38225 hom., cov: 30)
• Consequence: SYNAGE ENST00000643467.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248
• Publications: 3 publications found

Genes affected

SYNAGE (HGNC:56730):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643467.1. 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
	SYNAGE	ENST00000564048.2	TSL:6	n.136-10874A>T		intron	N/A
	SYNAGE	ENST00000623424.2	TSL:6	n.197-10874A>T		intron	N/A
	SYNAGE	ENST00000643467.1		n.659-10874A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.694 AC: 104881 AN: 151152 Hom.: 38168 Cov.: 30

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.694 AC: 104994 AN: 151268 Hom.: 38225 Cov.: 30 AF XY: 0.697 AC XY: 51500 AN XY: 73900

African (AFR) AF: 0.869 AC: 35978 AN: 41412

American (AMR) AF: 0.760 AC: 11575 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2322 AN: 3462

East Asian (EAS) AF: 0.983 AC: 5092 AN: 5178

South Asian (SAS) AF: 0.786 AC: 3773 AN: 4802

European-Finnish (FIN) AF: 0.498 AC: 5137 AN: 10312

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38788 AN: 67578

Other (OTH) AF: 0.721 AC: 1508 AN: 2092

Alfa AF: 0.601 Hom.: 3446

Bravo AF: 0.727

Asia WGS AF: 0.873 AC: 3028 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.1
DANN	Benign	0.82
PhyloP100		-0.25

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2216263;

hg19: chr16-49353504;