rs35399

chr5-33939790-T-C

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 0.0541 in 152,208 control chromosomes in the GnomAD database, including 434 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 0.054 (434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 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: 0.0540 AC: 8215 AN: 152090 Hom.: 432 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0715

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.00254

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0541 AC: 8232 AN: 152208 Hom.: 434 Cov.: 32 AF XY: 0.0567 AC XY: 4221 AN XY: 74404

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.0722

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.00254

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0307 Hom.: 62

Bravo AF: 0.0615

Asia WGS AF: 0.188 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.85
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35399; hg19: chr5-33939895;