rs10516564

chr4-110818136-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 0.251 in 151,864 control chromosomes in the GnomAD database, including 5,211 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 0.25 (5211 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.303 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: 0.251 AC: 38050 AN: 151746 Hom.: 5209 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.251 AC: 38071 AN: 151864 Hom.: 5211 Cov.: 32 AF XY: 0.247 AC XY: 18316 AN XY: 74244

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.270

Alfa AF: 0.291 Hom.: 5685

Bravo AF: 0.251

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.4
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516564; hg19: chr4-111739292;