rs6865651

Variant summary

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

The XR_007058906.1(LOC124901047):​n.2086-82177C>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 0.182 in 152,096 control chromosomes in the GnomAD database, including 2,804 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 0.18 ( 2804 hom., cov: 32)

Consequence

LOC124901047
XR_007058906.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.115
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=-0.94).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124901047XR_007058906.1 linkuse as main transcriptn.2086-82177C>T intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.182
AC:
27680
AN:
151978
Hom.:
2805
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.102
Gnomad AMI
AF:
0.310
Gnomad AMR
AF:
0.171
Gnomad ASJ
AF:
0.172
Gnomad EAS
AF:
0.141
Gnomad SAS
AF:
0.228
Gnomad FIN
AF:
0.296
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.215
Gnomad OTH
AF:
0.165
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.182
AC:
27683
AN:
152096
Hom.:
2804
Cov.:
32
AF XY:
0.186
AC XY:
13847
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.102
Gnomad4 AMR
AF:
0.171
Gnomad4 ASJ
AF:
0.172
Gnomad4 EAS
AF:
0.141
Gnomad4 SAS
AF:
0.227
Gnomad4 FIN
AF:
0.296
Gnomad4 NFE
AF:
0.215
Gnomad4 OTH
AF:
0.164
Alfa
AF:
0.196
Hom.:
472
Bravo
AF:
0.169
Asia WGS
AF:
0.185
AC:
640
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.6
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: rs6865651; hg19: chr5-113251696; COSMIC: COSV60183802; API