rs10516308

Variant names:

• chr4-17102559-C-T
• rs10516308

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.370 AC: 15329 AN: 41398

American (AMR) AF: 0.437 AC: 6661 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1419 AN: 3464

East Asian (EAS) AF: 0.272 AC: 1399 AN: 5148

South Asian (SAS) AF: 0.390 AC: 1880 AN: 4820

European-Finnish (FIN) AF: 0.447 AC: 4695 AN: 10512

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29631 AN: 67934

Other (OTH) AF: 0.387 AC: 818 AN: 2114

Alfa AF: 0.440 Hom.: 1919

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
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs10516308; hg19: chr4-17104182;