rs10516213

Variant names:

• chr4-10870031-A-C
• rs10516213

Your query was ambiguous. Multiple possible variants found:

• chr4-10870031-A-C
• chr4-10870031-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.135 in 152,204 control chromosomes in the GnomAD database, including 1,466 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 (1466 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.177 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: 20490 AN: 152086 Hom.: 1466 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.135 AC: 20491 AN: 152204 Hom.: 1466 Cov.: 32 AF XY: 0.135 AC XY: 10076 AN XY: 74402

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0563

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.154

Alfa AF: 0.133 Hom.: 1968

Bravo AF: 0.132

Asia WGS AF: 0.122 AC: 427 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	2.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516213; hg19: chr4-10871655;