rs11691711

Variant names:

• chr2-184429189-G-A
• rs11691711
• XR_001739819.1:n.319-4126G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-184429189-G-A
• chr2-184429189-G-T

Variant summary

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

The XR_001739819.1(LOC102724340):​n.319-4126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,662 control chromosomes in the GnomAD database, including 4,516 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 (4516 hom., cov: 32)
• Consequence: LOC102724340 XR_001739819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 2 publications found

Genes affected

LOC102724340 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 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: 0.223 AC: 33753 AN: 151544 Hom.: 4518 Cov.: 32

Gnomad AFR AF: 0.0996

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.223 AC: 33761 AN: 151662 Hom.: 4516 Cov.: 32 AF XY: 0.229 AC XY: 16956 AN XY: 74102

African (AFR) AF: 0.0995 AC: 4121 AN: 41406

American (AMR) AF: 0.346 AC: 5276 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 925 AN: 3468

East Asian (EAS) AF: 0.552 AC: 2851 AN: 5166

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4826

European-Finnish (FIN) AF: 0.252 AC: 2643 AN: 10474

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15958 AN: 67794

Other (OTH) AF: 0.224 AC: 470 AN: 2096

Alfa AF: 0.240 Hom.: 1406

Bravo AF: 0.225

Asia WGS AF: 0.334 AC: 1147 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.16
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11691711; hg19: chr2-185293916;