rs11860394

Variant names:

• chr16-55292892-A-G
• rs11860394
• ENST00000558730.2:n.89-10228T>C

Your query was ambiguous. Multiple possible variants found:

• chr16-55292892-A-G
• chr16-55292892-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558730.2(ENSG00000259283):​n.89-10228T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,598 control chromosomes in the GnomAD database, including 11,803 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 0.39 (11803 hom., cov: 30)
• Consequence: ENSG00000259283 ENST00000558730.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

Genes affected

ENSG00000259283 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.649 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
ENSG00000259283	ENST00000558730.2	n.89-10228T>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58910 AN: 151480 Hom.: 11790 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.389 AC: 58964 AN: 151598 Hom.: 11803 Cov.: 30 AF XY: 0.393 AC XY: 29074 AN XY: 74026

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.384

Alfa AF: 0.357 Hom.: 20010

Bravo AF: 0.392

Asia WGS AF: 0.563 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.42
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11860394; hg19: chr16-55326804;