rs10516346

Variant names:

• chr4-20116450-A-C
• rs10516346

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 0.231 in 151,992 control chromosomes in the GnomAD database, including 4,599 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 0.23 (4599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 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: 0.231 AC: 35106 AN: 151874 Hom.: 4581 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0944

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.231 AC: 35176 AN: 151992 Hom.: 4599 Cov.: 32 AF XY: 0.228 AC XY: 16902 AN XY: 74290

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0949

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.211

Alfa AF: 0.191 Hom.: 4199

Bravo AF: 0.237

Asia WGS AF: 0.180 AC: 622 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516346; hg19: chr4-20118073;