rs284744

Variant names:

• chr5-35470186-T-G
• rs284744

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;