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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724340	XR_001739819.1	n.319-4126G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;