5-166262722-A-C

Variant names:

• chr5-166262722-A-C
• rs10516012

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 0.378 in 152,028 control chromosomes in the GnomAD database, including 11,556 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 0.38 (11556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.818
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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: 0.378 AC: 57462 AN: 151910 Hom.: 11551 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.378 AC: 57488 AN: 152028 Hom.: 11556 Cov.: 32 AF XY: 0.369 AC XY: 27428 AN XY: 74322

African (AFR) AF: 0.296 AC: 12284 AN: 41478

American (AMR) AF: 0.305 AC: 4666 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1841 AN: 3468

East Asian (EAS) AF: 0.212 AC: 1099 AN: 5176

South Asian (SAS) AF: 0.393 AC: 1896 AN: 4820

European-Finnish (FIN) AF: 0.321 AC: 3387 AN: 10548

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31065 AN: 67942

Other (OTH) AF: 0.384 AC: 812 AN: 2112

Alfa AF: 0.426 Hom.: 1794

Bravo AF: 0.370

Asia WGS AF: 0.294 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	16
DANN	Benign	0.77
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs10516012; hg19: chr5-165689727;