16-20220513-G-A

Variant names:

• chr16-20220513-G-A
• rs4399544
• ENST00000804517.1:n.540C>T

Variant summary

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

The ENST00000804517.1(ENSG00000304556):​n.540C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,958 control chromosomes in the GnomAD database, including 19,217 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 0.48 (19217 hom., cov: 32)
• Consequence: ENSG00000304556 ENST00000804517.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 3 publications found

Genes affected

ENSG00000304556 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804517.1. 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
	ENSG00000304556	ENST00000804517.1		n.540C>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72229 AN: 151840 Hom.: 19217 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.475 AC: 72240 AN: 151958 Hom.: 19217 Cov.: 32 AF XY: 0.476 AC XY: 35341 AN XY: 74246

African (AFR) AF: 0.226 AC: 9367 AN: 41476

American (AMR) AF: 0.543 AC: 8291 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2077 AN: 3472

East Asian (EAS) AF: 0.590 AC: 3035 AN: 5148

South Asian (SAS) AF: 0.581 AC: 2792 AN: 4808

European-Finnish (FIN) AF: 0.496 AC: 5223 AN: 10522

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39542 AN: 67948

Other (OTH) AF: 0.530 AC: 1115 AN: 2104

Alfa AF: 0.515 Hom.: 3582

Bravo AF: 0.466

Asia WGS AF: 0.536 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	13
DANN	Benign	0.69
PhyloP100		0.034

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: rs4399544;

hg19: chr16-20231835;