rs10516346

chr4-20116450-A-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;