16-86681109-G-C

Variant names:

• chr16-86681109-G-C
• rs71390846
• ENST00000808928.1:n.855-15064G>C

Variant summary

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

The ENST00000808928.1(ENSG00000261161):​n.855-15064G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 151,912 control chromosomes in the GnomAD database, including 1,910 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 0.15 (1910 hom., cov: 32)
• Consequence: ENSG00000261161 ENST00000808928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 23 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 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
ENSG00000261161	ENST00000808928.1	n.855-15064G>C		intron_variant	Intron 4 of 4
ENSG00000261161	ENST00000808929.1	n.722-15064G>C		intron_variant	Intron 5 of 5
ENSG00000261161	ENST00000808930.1	n.114-15064G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22293 AN: 151794 Hom.: 1912 Cov.: 32

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.147 AC: 22281 AN: 151912 Hom.: 1910 Cov.: 32 AF XY: 0.148 AC XY: 10979 AN XY: 74242

African (AFR) AF: 0.0690 AC: 2859 AN: 41442

American (AMR) AF: 0.0948 AC: 1448 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3468

East Asian (EAS) AF: 0.296 AC: 1513 AN: 5114

South Asian (SAS) AF: 0.134 AC: 644 AN: 4810

European-Finnish (FIN) AF: 0.219 AC: 2309 AN: 10566

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12259 AN: 67918

Other (OTH) AF: 0.137 AC: 289 AN: 2110

Alfa AF: 0.0788 Hom.: 110

Bravo AF: 0.136

Asia WGS AF: 0.178 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.085
DANN	Benign	0.65
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs71390846; hg19: chr16-86714715;