rs9310784

Variant summary

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

The XR_007095849.1(LOC124909357):​n.226+14710T>C 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 0.201 in 152,136 control chromosomes in the GnomAD database, including 3,718 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 ( 3718 hom., cov: 32)

Consequence

LOC124909357
XR_007095849.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0700
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 (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124909357XR_007095849.1 linkuse as main transcriptn.226+14710T>C intron_variant, non_coding_transcript_variant
LOC124909357XR_007095848.1 linkuse as main transcriptn.123+14813T>C intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.201
AC:
30557
AN:
152018
Hom.:
3714
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.335
Gnomad AMI
AF:
0.207
Gnomad AMR
AF:
0.141
Gnomad ASJ
AF:
0.127
Gnomad EAS
AF:
0.0399
Gnomad SAS
AF:
0.253
Gnomad FIN
AF:
0.156
Gnomad MID
AF:
0.123
Gnomad NFE
AF:
0.154
Gnomad OTH
AF:
0.177
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.201
AC:
30578
AN:
152136
Hom.:
3718
Cov.:
32
AF XY:
0.200
AC XY:
14841
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.335
Gnomad4 AMR
AF:
0.140
Gnomad4 ASJ
AF:
0.127
Gnomad4 EAS
AF:
0.0394
Gnomad4 SAS
AF:
0.252
Gnomad4 FIN
AF:
0.156
Gnomad4 NFE
AF:
0.154
Gnomad4 OTH
AF:
0.175
Alfa
AF:
0.164
Hom.:
1299
Bravo
AF:
0.205
Asia WGS
AF:
0.209
AC:
728
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.0
DANN
Benign
0.67

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: rs9310784; hg19: chr3-25930204; API