16-69529987-C-T

Variant names:

• chr16-69529987-C-T
• rs7193778
• ENST00000720576.1:n.254+549G>A

Variant summary

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

The ENST00000720576.1(ENSG00000294014):​n.254+549G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 152,252 control chromosomes in the GnomAD database, including 61,596 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 0.90 (61596 hom., cov: 32)
• Consequence: ENSG00000294014 ENST00000720576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 41 publications found

Genes affected

ENSG00000294014 (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 = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294014	ENST00000720576.1	n.254+549G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.898 AC: 136583 AN: 152134 Hom.: 61538 Cov.: 32

Gnomad AFR AF: 0.974

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.898 AC: 136699 AN: 152252 Hom.: 61596 Cov.: 32 AF XY: 0.899 AC XY: 66942 AN XY: 74432

African (AFR) AF: 0.974 AC: 40481 AN: 41554

American (AMR) AF: 0.877 AC: 13403 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3171 AN: 3472

East Asian (EAS) AF: 0.940 AC: 4872 AN: 5182

South Asian (SAS) AF: 0.872 AC: 4210 AN: 4828

European-Finnish (FIN) AF: 0.868 AC: 9196 AN: 10590

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58468 AN: 68020

Other (OTH) AF: 0.892 AC: 1887 AN: 2116

Alfa AF: 0.879 Hom.: 97598

Bravo AF: 0.900

Asia WGS AF: 0.911 AC: 3170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.11
DANN	Benign	0.79
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs7193778; hg19: chr16-69563890;