rs861085

Variant names:

• chr5-103583104-G-A
• rs861085

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 0.47 in 151,720 control chromosomes in the GnomAD database, including 21,939 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 0.47 (21939 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 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: 0.469 AC: 71152 AN: 151604 Hom.: 21893 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.400

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.470 AC: 71254 AN: 151720 Hom.: 21939 Cov.: 32 AF XY: 0.471 AC XY: 34952 AN XY: 74168

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.435

Alfa AF: 0.333 Hom.: 6018

Bravo AF: 0.497

Asia WGS AF: 0.779 AC: 2696 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
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: rs861085; hg19: chr5-102918805;