rs16940186

Positions:

• chr16-85976134-T-C

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, non coding transcript 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: ENST00000645754.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000645754.1	n.227+8308A>G		intron_variant, non_coding_transcript_variant

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;