rs2888830

Variant summary

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

The XR_007060425.1(LOC124901695):​n.126+1268C>T 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 0.645 in 152,048 control chromosomes in the GnomAD database, including 31,754 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 0.64 ( 31754 hom., cov: 32)

Consequence

LOC124901695
XR_007060425.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0570
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=-0.85).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124901695XR_007060425.1 linkuse as main transcriptn.126+1268C>T intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.645
AC:
97961
AN:
151930
Hom.:
31744
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.586
Gnomad AMI
AF:
0.758
Gnomad AMR
AF:
0.683
Gnomad ASJ
AF:
0.627
Gnomad EAS
AF:
0.639
Gnomad SAS
AF:
0.629
Gnomad FIN
AF:
0.632
Gnomad MID
AF:
0.734
Gnomad NFE
AF:
0.674
Gnomad OTH
AF:
0.651
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.645
AC:
97998
AN:
152048
Hom.:
31754
Cov.:
32
AF XY:
0.643
AC XY:
47806
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.586
Gnomad4 AMR
AF:
0.683
Gnomad4 ASJ
AF:
0.627
Gnomad4 EAS
AF:
0.639
Gnomad4 SAS
AF:
0.630
Gnomad4 FIN
AF:
0.632
Gnomad4 NFE
AF:
0.674
Gnomad4 OTH
AF:
0.644
Alfa
AF:
0.674
Hom.:
32821
Bravo
AF:
0.649
Asia WGS
AF:
0.559
AC:
1945
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.6
DANN
Benign
0.78

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: rs2888830; hg19: chr7-90915354; API