rs3852160

chr5-5822534-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 0.623 in 152,008 control chromosomes in the GnomAD database, including 29,581 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 0.62 (29581 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 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: 0.623 AC: 94580 AN: 151888 Hom.: 29552 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.623 AC: 94653 AN: 152008 Hom.: 29581 Cov.: 32 AF XY: 0.624 AC XY: 46342 AN XY: 74292

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.625

Alfa AF: 0.603 Hom.: 26824

Bravo AF: 0.627

Asia WGS AF: 0.611 AC: 2127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.51
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3852160; hg19: chr5-5822647;