5-111067057-C-A

Variant names:

• chr5-111067057-C-A
• rs12654933

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 0.135 in 152,134 control chromosomes in the GnomAD database, including 2,153 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 0.13 (2153 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 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: 0.135 AC: 20489 AN: 152014 Hom.: 2144 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0304

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0568

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.135 AC: 20534 AN: 152134 Hom.: 2153 Cov.: 33 AF XY: 0.135 AC XY: 10029 AN XY: 74380

African (AFR) AF: 0.284 AC: 11756 AN: 41456

American (AMR) AF: 0.153 AC: 2341 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3468

East Asian (EAS) AF: 0.201 AC: 1042 AN: 5178

South Asian (SAS) AF: 0.140 AC: 675 AN: 4820

European-Finnish (FIN) AF: 0.0304 AC: 322 AN: 10604

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0568 AC: 3865 AN: 68008

Other (OTH) AF: 0.112 AC: 236 AN: 2114

Alfa AF: 0.0816 Hom.: 1108

Bravo AF: 0.150

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.20
DANN	Benign	0.46
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs12654933; hg19: chr5-110402755;