5-35851159-G-T

Variant names:

• chr5-35851159-G-T
• rs12516866

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 0.397 in 151,966 control chromosomes in the GnomAD database, including 12,052 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 0.40 (12052 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.863

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 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: 0.397 AC: 60298 AN: 151850 Hom.: 12052 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.397 AC: 60320 AN: 151966 Hom.: 12052 Cov.: 32 AF XY: 0.397 AC XY: 29455 AN XY: 74260

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.378

Alfa AF: 0.397 Hom.: 1768

Bravo AF: 0.393

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.3
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12516866; hg19: chr5-35851261;