rs10914386

Variant summary

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

The XR_007065585.1(LOC124903900):​n.412-8616T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,958 control chromosomes in the GnomAD database, including 25,273 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 0.53 ( 25273 hom., cov: 32)

Consequence

LOC124903900
XR_007065585.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.673
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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124903900XR_007065585.1 linkuse as main transcriptn.412-8616T>G intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.531
AC:
80685
AN:
151840
Hom.:
25278
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.212
Gnomad AMI
AF:
0.800
Gnomad AMR
AF:
0.583
Gnomad ASJ
AF:
0.660
Gnomad EAS
AF:
0.221
Gnomad SAS
AF:
0.427
Gnomad FIN
AF:
0.682
Gnomad MID
AF:
0.604
Gnomad NFE
AF:
0.710
Gnomad OTH
AF:
0.569
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.531
AC:
80687
AN:
151958
Hom.:
25273
Cov.:
32
AF XY:
0.528
AC XY:
39242
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.211
Gnomad4 AMR
AF:
0.583
Gnomad4 ASJ
AF:
0.660
Gnomad4 EAS
AF:
0.221
Gnomad4 SAS
AF:
0.427
Gnomad4 FIN
AF:
0.682
Gnomad4 NFE
AF:
0.710
Gnomad4 OTH
AF:
0.566
Alfa
AF:
0.668
Hom.:
23991
Bravo
AF:
0.510

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.3
DANN
Benign
0.27

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: rs10914386; hg19: chr1-31909072; API