rs586701

Variant names:

• chr11-102853999-T-G
• rs586701
• XR_007062868.1:n.1527T>G

Variant summary

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

The XR_007062868.1(LOC124902741):​n.1527T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,098 control chromosomes in the GnomAD database, including 3,218 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 0.20 (3218 hom., cov: 32)
• Consequence: LOC124902741 XR_007062868.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• Publications: 12 publications found

Genes affected

LOC124902741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 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: 0.202 AC: 30671 AN: 151980 Hom.: 3214 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.202 AC: 30679 AN: 152098 Hom.: 3218 Cov.: 32 AF XY: 0.201 AC XY: 14959 AN XY: 74358

African (AFR) AF: 0.251 AC: 10407 AN: 41480

American (AMR) AF: 0.144 AC: 2203 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3470

East Asian (EAS) AF: 0.135 AC: 701 AN: 5180

South Asian (SAS) AF: 0.173 AC: 832 AN: 4822

European-Finnish (FIN) AF: 0.247 AC: 2612 AN: 10588

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.182 AC: 12385 AN: 67978

Other (OTH) AF: 0.201 AC: 423 AN: 2108

Alfa AF: 0.202 Hom.: 398

Bravo AF: 0.196

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.45
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs586701; hg19: chr11-102724730;