16-52313907-T-G

Variant names:

• chr16-52313907-T-G
• rs4784165
• ENST00000701553.1:n.332-14041A>C

Variant summary

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

The ENST00000701553.1(ENSG00000289907):​n.332-14041A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,028 control chromosomes in the GnomAD database, including 7,931 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 0.31 (7931 hom., cov: 32)
• Consequence: ENSG00000289907 ENST00000701553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 28 publications found

Genes affected

ENSG00000289907 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701553.1. 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
	ENSG00000289907	ENST00000701553.1		n.332-14041A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47294 AN: 151908 Hom.: 7906 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.312 AC: 47361 AN: 152028 Hom.: 7931 Cov.: 32 AF XY: 0.308 AC XY: 22867 AN XY: 74286

African (AFR) AF: 0.427 AC: 17718 AN: 41454

American (AMR) AF: 0.312 AC: 4760 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1340 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1885 AN: 5144

South Asian (SAS) AF: 0.266 AC: 1283 AN: 4816

European-Finnish (FIN) AF: 0.214 AC: 2262 AN: 10586

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17160 AN: 67966

Other (OTH) AF: 0.308 AC: 651 AN: 2114

Alfa AF: 0.274 Hom.: 14405

Bravo AF: 0.327

Asia WGS AF: 0.324 AC: 1125 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-0.0020

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: rs4784165;

hg19: chr16-52347819;