5-116423793-G-A

Variant names:

• chr5-116423793-G-A
• rs26595

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 0.441 in 152,024 control chromosomes in the GnomAD database, including 17,697 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 0.44 (17697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 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: 0.441 AC: 67021 AN: 151904 Hom.: 17701 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.441 AC: 67007 AN: 152024 Hom.: 17697 Cov.: 32 AF XY: 0.439 AC XY: 32641 AN XY: 74304

African (AFR) AF: 0.150 AC: 6212 AN: 41476

American (AMR) AF: 0.462 AC: 7063 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1813 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1263 AN: 5174

South Asian (SAS) AF: 0.445 AC: 2140 AN: 4812

European-Finnish (FIN) AF: 0.660 AC: 6969 AN: 10558

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39783 AN: 67942

Other (OTH) AF: 0.446 AC: 941 AN: 2112

Alfa AF: 0.524 Hom.: 78919

Bravo AF: 0.412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.69
DANN	Benign	0.65
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs26595; hg19: chr5-115759490;