rs11584885

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_007065348.1(LOC124903818):​n.805G>A 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 0.224 in 152,084 control chromosomes in the GnomAD database, including 4,381 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 ( 4381 hom., cov: 32)

Consequence

LOC124903818
XR_007065348.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00600
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124903818XR_007065348.1 linkuse as main transcriptn.805G>A non_coding_transcript_exon_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.224
AC:
34008
AN:
151966
Hom.:
4382
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.156
Gnomad AMI
AF:
0.267
Gnomad AMR
AF:
0.149
Gnomad ASJ
AF:
0.193
Gnomad EAS
AF:
0.0297
Gnomad SAS
AF:
0.202
Gnomad FIN
AF:
0.321
Gnomad MID
AF:
0.244
Gnomad NFE
AF:
0.285
Gnomad OTH
AF:
0.205
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.224
AC:
34023
AN:
152084
Hom.:
4381
Cov.:
32
AF XY:
0.223
AC XY:
16552
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.156
Gnomad4 AMR
AF:
0.148
Gnomad4 ASJ
AF:
0.193
Gnomad4 EAS
AF:
0.0296
Gnomad4 SAS
AF:
0.202
Gnomad4 FIN
AF:
0.321
Gnomad4 NFE
AF:
0.285
Gnomad4 OTH
AF:
0.202
Alfa
AF:
0.263
Hom.:
1107
Bravo
AF:
0.205
Asia WGS
AF:
0.105
AC:
363
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
6.6
DANN
Benign
0.85

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11584885; hg19: chr1-1099437; API