5-33405491-G-A

Position:

• chr5-33405491-G-A

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 0.167 in 152,048 control chromosomes in the GnomAD database, including 2,302 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 0.17 (2302 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

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 (EAS) allele frequency at 95% confidence interval = 0.258 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: 0.167 AC: 25310 AN: 151932 Hom.: 2299 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.167 AC: 25318 AN: 152048 Hom.: 2302 Cov.: 31 AF XY: 0.171 AC XY: 12742 AN XY: 74306

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.197

Alfa AF: 0.164 Hom.: 4442

Bravo AF: 0.172

Asia WGS AF: 0.253 AC: 881 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	0.64
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs268706; hg19: chr5-33405597;