rs7964748

Variant summary

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

The XR_007063427.1(LINC02456):​n.34902+87663A>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 0.226 in 151,922 control chromosomes in the GnomAD database, including 4,031 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 0.23 ( 4031 hom., cov: 31)

Consequence

LINC02456
XR_007063427.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.135
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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC02456XR_007063427.1 linkuse as main transcriptn.34902+87663A>G intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.226
AC:
34302
AN:
151804
Hom.:
4021
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.297
Gnomad AMI
AF:
0.247
Gnomad AMR
AF:
0.186
Gnomad ASJ
AF:
0.200
Gnomad EAS
AF:
0.177
Gnomad SAS
AF:
0.284
Gnomad FIN
AF:
0.231
Gnomad MID
AF:
0.307
Gnomad NFE
AF:
0.191
Gnomad OTH
AF:
0.225
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.226
AC:
34341
AN:
151922
Hom.:
4031
Cov.:
31
AF XY:
0.229
AC XY:
16970
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.297
Gnomad4 AMR
AF:
0.186
Gnomad4 ASJ
AF:
0.200
Gnomad4 EAS
AF:
0.177
Gnomad4 SAS
AF:
0.284
Gnomad4 FIN
AF:
0.231
Gnomad4 NFE
AF:
0.191
Gnomad4 OTH
AF:
0.221
Alfa
AF:
0.206
Hom.:
1496
Bravo
AF:
0.223
Asia WGS
AF:
0.215
AC:
747
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
1.5
DANN
Benign
0.51

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: rs7964748; hg19: chr12-102965329; API