16-54460512-A-G

Variant names:

• chr16-54460512-A-G
• rs9921518
• ENST00000720695.1:n.183-6328A>G

Variant summary

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

The ENST00000720695.1(ENSG00000287885):​n.183-6328A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 152,192 control chromosomes in the GnomAD database, including 44,974 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 0.77 (44974 hom., cov: 33)
• Consequence: ENSG00000287885 ENST00000720695.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 12 publications found

Genes affected

ENSG00000287885 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720695.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287885	ENST00000720695.1		n.183-6328A>G		intron	N/A
	ENSG00000287885	ENST00000720697.1		n.133-6328A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116616 AN: 152074 Hom.: 44944 Cov.: 33

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.767 AC: 116696 AN: 152192 Hom.: 44974 Cov.: 33 AF XY: 0.773 AC XY: 57533 AN XY: 74402

African (AFR) AF: 0.706 AC: 29318 AN: 41498

American (AMR) AF: 0.790 AC: 12094 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2336 AN: 3472

East Asian (EAS) AF: 0.950 AC: 4916 AN: 5176

South Asian (SAS) AF: 0.811 AC: 3900 AN: 4810

European-Finnish (FIN) AF: 0.859 AC: 9114 AN: 10608

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52586 AN: 68010

Other (OTH) AF: 0.764 AC: 1611 AN: 2110

Alfa AF: 0.772 Hom.: 157370

Bravo AF: 0.758

Asia WGS AF: 0.855 AC: 2971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.052
DANN	Benign	0.38
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9921518; hg19: chr16-54494424;