rs16940186

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 23 publications found

Genes affected

ENSG00000285040 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645754.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285040	ENST00000645754.1		n.227+8308A>G		intron	N/A
	ENSG00000294410	ENST00000723428.1		n.410-1401T>C		intron	N/A

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

African (AFR) AF: 0.144 AC: 5954 AN: 41244

American (AMR) AF: 0.178 AC: 2710 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1293 AN: 5160

South Asian (SAS) AF: 0.281 AC: 1349 AN: 4800

European-Finnish (FIN) AF: 0.147 AC: 1510 AN: 10282

Middle Eastern (MID) AF: 0.310 AC: 90 AN: 290

European-Non Finnish (NFE) AF: 0.164 AC: 11099 AN: 67872

Other (OTH) AF: 0.200 AC: 421 AN: 2102

Alfa AF: 0.171 Hom.: 8671

Bravo AF: 0.171

Asia WGS AF: 0.257 AC: 888 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.36
PhyloP100		-0.10

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16940186;

hg19: chr16-86009740;