rs284744

chr5-35470186-T-G

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 0.327 in 152,206 control chromosomes in the GnomAD database, including 10,462 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 0.33 (10462 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

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 = 0.566 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: 0.326 AC: 49640 AN: 152088 Hom.: 10412 Cov.: 33

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.327 AC: 49753 AN: 152206 Hom.: 10462 Cov.: 33 AF XY: 0.328 AC XY: 24389 AN XY: 74430

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.307

Alfa AF: 0.246 Hom.: 1115

Bravo AF: 0.352

Asia WGS AF: 0.436 AC: 1518 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	5.1
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs284744; hg19: chr5-35470288;