16-52549231-C-T

Variant names:

• chr16-52549231-C-T
• rs4784226
• ENST00000826650.1:n.102+2719C>T

Variant summary

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

The ENST00000826650.1(ENSG00000285800):​n.102+2719C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,120 control chromosomes in the GnomAD database, including 3,587 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 0.20 (3587 hom., cov: 32)
• Consequence: ENSG00000285800 ENST00000826650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577
• Publications: 7 publications found

Genes affected

ENSG00000285800 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826650.1. 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
	ENSG00000285800	ENST00000826650.1		n.102+2719C>T		intron	N/A
	ENSG00000285800	ENST00000826651.1		n.89+2719C>T		intron	N/A
	ENSG00000285800	ENST00000826652.1		n.104+2671C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30298 AN: 152002 Hom.: 3580 Cov.: 32

Gnomad AFR AF: 0.0657

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.199 AC: 30321 AN: 152120 Hom.: 3587 Cov.: 32 AF XY: 0.201 AC XY: 14971 AN XY: 74370

African (AFR) AF: 0.0656 AC: 2724 AN: 41524

American (AMR) AF: 0.294 AC: 4490 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1257 AN: 5170

South Asian (SAS) AF: 0.191 AC: 922 AN: 4828

European-Finnish (FIN) AF: 0.247 AC: 2605 AN: 10556

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16429 AN: 67968

Other (OTH) AF: 0.238 AC: 503 AN: 2110

Alfa AF: 0.240 Hom.: 1909

Bravo AF: 0.198

Asia WGS AF: 0.229 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.73
PhyloP100		0.58

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: rs4784226;

hg19: chr16-52583143;