16-86773205-C-G

Variant names:

• chr16-86773205-C-G
• rs186172
• XR_001752396.2:n.3048C>G

Variant summary

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

The XR_001752396.2(LOC107984819):​n.3048C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,126 control chromosomes in the GnomAD database, including 2,936 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 0.15 (2936 hom., cov: 33)
• Consequence: LOC107984819 XR_001752396.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 0 publications found

Genes affected

LOC107984819 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22240 AN: 152008 Hom.: 2925 Cov.: 33

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.0910

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.147 AC: 22290 AN: 152126 Hom.: 2936 Cov.: 33 AF XY: 0.156 AC XY: 11593 AN XY: 74378

African (AFR) AF: 0.266 AC: 11029 AN: 41472

American (AMR) AF: 0.254 AC: 3876 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0893 AC: 310 AN: 3470

East Asian (EAS) AF: 0.475 AC: 2439 AN: 5138

South Asian (SAS) AF: 0.218 AC: 1053 AN: 4822

European-Finnish (FIN) AF: 0.0910 AC: 965 AN: 10602

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0330 AC: 2243 AN: 68014

Other (OTH) AF: 0.146 AC: 308 AN: 2114

Alfa AF: 0.0236 Hom.: 23

Bravo AF: 0.168

Asia WGS AF: 0.348 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.76
DANN	Benign	0.47
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs186172; hg19: chr16-86806811;