rs841086

Variant names:

• chr2-128530099-G-A
• rs841086
• XR_923318.2:n.2388-91252G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_923318.2(LOC105373611):​n.2388-91252G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,102 control chromosomes in the GnomAD database, including 7,061 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 0.22 (7061 hom., cov: 32)
• Consequence: LOC105373611 XR_923318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571
• Publications: 2 publications found

Genes affected

LOC105373611 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 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: 0.218 AC: 33202 AN: 151984 Hom.: 7028 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0318

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.0564

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.219 AC: 33297 AN: 152102 Hom.: 7061 Cov.: 32 AF XY: 0.213 AC XY: 15824 AN XY: 74386

African (AFR) AF: 0.559 AC: 23165 AN: 41436

American (AMR) AF: 0.143 AC: 2188 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3470

East Asian (EAS) AF: 0.0313 AC: 162 AN: 5178

South Asian (SAS) AF: 0.0843 AC: 407 AN: 4826

European-Finnish (FIN) AF: 0.0564 AC: 598 AN: 10604

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0868 AC: 5904 AN: 67980

Other (OTH) AF: 0.206 AC: 436 AN: 2114

Alfa AF: 0.125 Hom.: 1794

Bravo AF: 0.240

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.34
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs841086; hg19: chr2-129287673;