16-1031188-G-A

Variant names:

• chr16-1031188-G-A
• rs453169

Variant summary

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

The variant allele was found at a frequency of 0.0735 in 152,296 control chromosomes in the GnomAD database, including 499 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 0.073 (499 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 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

Frequencies

GnomAD3 genomes AF: 0.0735 AC: 11183 AN: 152178 Hom.: 499 Cov.: 33

Gnomad AFR AF: 0.0465

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0735 AC: 11190 AN: 152296 Hom.: 499 Cov.: 33 AF XY: 0.0738 AC XY: 5495 AN XY: 74468

African (AFR) AF: 0.0464 AC: 1930 AN: 41568

American (AMR) AF: 0.0504 AC: 771 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3470

East Asian (EAS) AF: 0.00348 AC: 18 AN: 5178

South Asian (SAS) AF: 0.117 AC: 565 AN: 4828

European-Finnish (FIN) AF: 0.0925 AC: 982 AN: 10616

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0929 AC: 6318 AN: 68014

Other (OTH) AF: 0.0696 AC: 147 AN: 2112

Alfa AF: 0.0861 Hom.: 528

Bravo AF: 0.0666

Asia WGS AF: 0.0530 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.66
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs453169; hg19: chr16-1081188;