rs11117425

Variant names:

• chr16-85938665-C-T
• rs11117425
• ENST00000645383.1:n.393+6391C>T

Variant summary

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

The ENST00000645383.1(ENSG00000285163):​n.393+6391C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,104 control chromosomes in the GnomAD database, including 8,652 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 0.33 (8652 hom., cov: 33)
• Consequence: ENSG00000285163 ENST00000645383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.21
• Publications: 9 publications found

Genes affected

ENSG00000285163 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 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
ENSG00000285163	ENST00000645383.1	n.393+6391C>T		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646214.1	n.78-6751C>T		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646986.2	n.715+2654C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50891 AN: 151986 Hom.: 8639 Cov.: 33

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.335 AC: 50931 AN: 152104 Hom.: 8652 Cov.: 33 AF XY: 0.336 AC XY: 25000 AN XY: 74340

African (AFR) AF: 0.327 AC: 13560 AN: 41492

American (AMR) AF: 0.395 AC: 6041 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3468

East Asian (EAS) AF: 0.424 AC: 2191 AN: 5172

South Asian (SAS) AF: 0.353 AC: 1700 AN: 4820

European-Finnish (FIN) AF: 0.353 AC: 3732 AN: 10564

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21666 AN: 67984

Other (OTH) AF: 0.325 AC: 686 AN: 2114

Alfa AF: 0.319 Hom.: 24636

Bravo AF: 0.335

Asia WGS AF: 0.388 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.66
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs11117425; hg19: chr16-85972271;