chr16-86677054-A-G

Variant names:

• chr16-86677054-A-G
• rs10048146
• ENST00000808928.1:n.855-19119A>G

Variant summary

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

The ENST00000808928.1(ENSG00000261161):​n.855-19119A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,100 control chromosomes in the GnomAD database, including 2,244 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 0.17 (2244 hom., cov: 31)
• Consequence: ENSG00000261161 ENST00000808928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 45 publications found

Genes affected

ENSG00000261161 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808928.1. 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
	ENSG00000261161	ENST00000808928.1		n.855-19119A>G		intron	N/A
	ENSG00000261161	ENST00000808929.1		n.722-19119A>G		intron	N/A
	ENSG00000261161	ENST00000808930.1		n.114-19119A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25277 AN: 151982 Hom.: 2248 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.166 AC: 25270 AN: 152100 Hom.: 2244 Cov.: 31 AF XY: 0.166 AC XY: 12324 AN XY: 74356

African (AFR) AF: 0.129 AC: 5367 AN: 41510

American (AMR) AF: 0.120 AC: 1827 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3472

East Asian (EAS) AF: 0.290 AC: 1493 AN: 5144

South Asian (SAS) AF: 0.137 AC: 660 AN: 4810

European-Finnish (FIN) AF: 0.208 AC: 2202 AN: 10574

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12492 AN: 67982

Other (OTH) AF: 0.152 AC: 322 AN: 2116

Alfa AF: 0.179 Hom.: 11212

Bravo AF: 0.161

Asia WGS AF: 0.175 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.30
DANN	Benign	0.44
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10048146; hg19: chr16-86710660;