rs10520939

Variant names:

• chr5-27934279-G-A
• rs10520939

Your query was ambiguous. Multiple possible variants found:

• chr5-27934279-G-A
• chr5-27934279-G-C

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 0.166 in 151,844 control chromosomes in the GnomAD database, including 2,873 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 0.17 (2873 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 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: 0.166 AC: 25128 AN: 151724 Hom.: 2860 Cov.: 32

Gnomad AFR AF: 0.0579

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.166 AC: 25152 AN: 151844 Hom.: 2873 Cov.: 32 AF XY: 0.172 AC XY: 12757 AN XY: 74182

African (AFR) AF: 0.0578 AC: 2394 AN: 41444

American (AMR) AF: 0.346 AC: 5264 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3466

East Asian (EAS) AF: 0.419 AC: 2164 AN: 5164

South Asian (SAS) AF: 0.252 AC: 1215 AN: 4820

European-Finnish (FIN) AF: 0.133 AC: 1396 AN: 10504

Middle Eastern (MID) AF: 0.177 AC: 51 AN: 288

European-Non Finnish (NFE) AF: 0.170 AC: 11529 AN: 67906

Other (OTH) AF: 0.179 AC: 379 AN: 2112

Alfa AF: 0.159 Hom.: 313

Bravo AF: 0.181

Asia WGS AF: 0.292 AC: 1002 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.31
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs10520939; hg19: chr5-27934386;