rs10516308

Positions:

• chr4-17102559-C-T

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 0.412 in 151,850 control chromosomes in the GnomAD database, including 12,954 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 0.41 (12954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.432 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: 0.412 AC: 62452 AN: 151732 Hom.: 12940 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.412 AC: 62507 AN: 151850 Hom.: 12954 Cov.: 32 AF XY: 0.410 AC XY: 30457 AN XY: 74226

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.387

Alfa AF: 0.443 Hom.: 1860

Bravo AF: 0.411

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516308; hg19: chr4-17104182;