rs16940186

Variant names:

• chr16-85976134-T-C
• rs16940186
• ENST00000645754.1:n.227+8308A>G

Variant summary

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

The ENST00000645754.1(ENSG00000285040):​n.227+8308A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 151,348 control chromosomes in the GnomAD database, including 2,362 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 (2362 hom., cov: 32)
• Consequence: ENSG00000285040 ENST00000645754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

Genes affected

ENSG00000285040 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 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
ENSG00000285040	ENST00000645754.1	n.227+8308A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25803 AN: 151242 Hom.: 2356 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.171 AC: 25823 AN: 151348 Hom.: 2362 Cov.: 32 AF XY: 0.172 AC XY: 12751 AN XY: 73928

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.200

Alfa AF: 0.176 Hom.: 4119

Bravo AF: 0.171

Asia WGS AF: 0.257 AC: 888 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16940186; hg19: chr16-86009740;