rs453169

chr16-1031188-G-Achr16-1031188-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0464

Gnomad4 AMR AF: 0.0504

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.00348

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0925

Gnomad4 NFE AF: 0.0929

Gnomad4 OTH AF: 0.0696

Alfa AF: 0.0842 Hom.: 353

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs453169; hg19: chr16-1081188;