rs284737

Variant names:

• chr5-35461098-T-C
• rs284737

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 0.546 in 152,040 control chromosomes in the GnomAD database, including 25,534 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 0.55 (25534 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.545 AC: 82826 AN: 151924 Hom.: 25469 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.546 AC: 82955 AN: 152040 Hom.: 25534 Cov.: 32 AF XY: 0.551 AC XY: 40932 AN XY: 74332

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.516

Alfa AF: 0.424 Hom.: 14331

Bravo AF: 0.562

Asia WGS AF: 0.729 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs284737; hg19: chr5-35461200;