16-1134967-G-A

Variant names:

• chr16-1134967-G-A
• rs11865472

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 0.42 in 152,146 control chromosomes in the GnomAD database, including 14,410 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 0.42 (14410 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.842
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 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: 0.420 AC: 63833 AN: 152028 Hom.: 14414 Cov.: 34

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.420 AC: 63848 AN: 152146 Hom.: 14410 Cov.: 34 AF XY: 0.416 AC XY: 30951 AN XY: 74380

African (AFR) AF: 0.284 AC: 11808 AN: 41526

American (AMR) AF: 0.382 AC: 5838 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2221 AN: 3472

East Asian (EAS) AF: 0.228 AC: 1175 AN: 5162

South Asian (SAS) AF: 0.451 AC: 2176 AN: 4830

European-Finnish (FIN) AF: 0.482 AC: 5107 AN: 10594

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33823 AN: 67958

Other (OTH) AF: 0.456 AC: 964 AN: 2112

Alfa AF: 0.477 Hom.: 37623

Bravo AF: 0.404

Asia WGS AF: 0.330 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.69
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs11865472; hg19: chr16-1184967;