5-35577155-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 0.538 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;