rs9285863

Positions:

• chr5-108735954-T-C

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 0.435 in 152,176 control chromosomes in the GnomAD database, including 17,159 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 0.43 (17159 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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 = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66072 AN: 152058 Hom.: 17112 Cov.: 33

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.435 AC: 66169 AN: 152176 Hom.: 17159 Cov.: 33 AF XY: 0.426 AC XY: 31674 AN XY: 74416

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.404

Alfa AF: 0.380 Hom.: 2493

Bravo AF: 0.446

Asia WGS AF: 0.301 AC: 1047 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	1.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9285863; hg19: chr5-108071655;