rs368855

Variant summary

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

The XR_007064276.1(LOC124903351):​n.1324+361C>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 0.236 in 152,128 control chromosomes in the GnomAD database, including 4,786 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 0.24 ( 4786 hom., cov: 33)

Consequence

LOC124903351
XR_007064276.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05
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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124903351XR_007064276.1 linkuse as main transcriptn.1324+361C>T intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.236
AC:
35867
AN:
152010
Hom.:
4777
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.197
Gnomad AMI
AF:
0.290
Gnomad AMR
AF:
0.313
Gnomad ASJ
AF:
0.299
Gnomad EAS
AF:
0.592
Gnomad SAS
AF:
0.304
Gnomad FIN
AF:
0.188
Gnomad MID
AF:
0.196
Gnomad NFE
AF:
0.214
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.236
AC:
35902
AN:
152128
Hom.:
4786
Cov.:
33
AF XY:
0.241
AC XY:
17914
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.197
Gnomad4 AMR
AF:
0.313
Gnomad4 ASJ
AF:
0.299
Gnomad4 EAS
AF:
0.591
Gnomad4 SAS
AF:
0.305
Gnomad4 FIN
AF:
0.188
Gnomad4 NFE
AF:
0.214
Gnomad4 OTH
AF:
0.254
Alfa
AF:
0.229
Hom.:
2541
Bravo
AF:
0.248
Asia WGS
AF:
0.391
AC:
1363
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.37
DANN
Benign
0.48

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: rs368855; hg19: chr14-77727846; API