rs861085

Variant names:

• chr5-103583104-G-A
• rs861085

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.825 AC: 34237 AN: 41492

American (AMR) AF: 0.388 AC: 5897 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1213 AN: 3464

East Asian (EAS) AF: 0.941 AC: 4862 AN: 5168

South Asian (SAS) AF: 0.641 AC: 3095 AN: 4828

European-Finnish (FIN) AF: 0.201 AC: 2131 AN: 10576

Middle Eastern (MID) AF: 0.417 AC: 120 AN: 288

European-Non Finnish (NFE) AF: 0.272 AC: 18439 AN: 67668

Other (OTH) AF: 0.435 AC: 917 AN: 2106

Alfa AF: 0.330 Hom.: 6424

Bravo AF: 0.497

Asia WGS AF: 0.779 AC: 2696 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
DANN	Benign	0.74
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs861085; hg19: chr5-102918805;