ENST00000808928.1:n.855-2480A>G

Variant names:

• chr16-86693693-A-G
• rs11866031
• ENST00000808928.1:n.855-2480A>G

Variant summary

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

The ENST00000808928.1(ENSG00000261161):​n.855-2480A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,074 control chromosomes in the GnomAD database, including 5,311 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 0.22 (5311 hom., cov: 32)
• Consequence: ENSG00000261161 ENST00000808928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 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.855-2480A>G		intron_variant	Intron 4 of 4
ENSG00000261161	ENST00000808929.1	n.722-2480A>G		intron_variant	Intron 5 of 5
ENSG00000261161	ENST00000808930.1	n.114-2480A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34117 AN: 151956 Hom.: 5292 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0569

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.225 AC: 34186 AN: 152074 Hom.: 5311 Cov.: 32 AF XY: 0.222 AC XY: 16504 AN XY: 74344

African (AFR) AF: 0.437 AC: 18103 AN: 41450

American (AMR) AF: 0.250 AC: 3817 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 477 AN: 3472

East Asian (EAS) AF: 0.0564 AC: 292 AN: 5174

South Asian (SAS) AF: 0.128 AC: 614 AN: 4812

European-Finnish (FIN) AF: 0.106 AC: 1122 AN: 10580

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9096 AN: 67998

Other (OTH) AF: 0.210 AC: 444 AN: 2116

Alfa AF: 0.157 Hom.: 1402

Bravo AF: 0.246

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.29
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs11866031; hg19: chr16-86727299;