5-35577155-C-T

Variant names:

• chr5-35577155-C-T
• rs286405

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 0.538 in 151,730 control chromosomes in the GnomAD database, including 23,278 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 0.54 (23278 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 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: 0.538 AC: 81516 AN: 151612 Hom.: 23228 Cov.: 33

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.538 AC: 81624 AN: 151730 Hom.: 23278 Cov.: 33 AF XY: 0.543 AC XY: 40272 AN XY: 74134

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.511

Alfa AF: 0.475 Hom.: 7033

Bravo AF: 0.549

Asia WGS AF: 0.669 AC: 2323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs286405; hg19: chr5-35577257;