rs2225614

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The XR_007061897.1(LOC124902327):​n.96-35154C>A 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 152,120 control chromosomes in the GnomAD database, including 3,773 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 ( 3773 hom., cov: 32)

Consequence

LOC124902327
XR_007061897.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.156
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.27).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124902327XR_007061897.1 linkuse as main transcriptn.96-35154C>A 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:
30550
AN:
152002
Hom.:
3762
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.133
Gnomad AMI
AF:
0.105
Gnomad AMR
AF:
0.252
Gnomad ASJ
AF:
0.273
Gnomad EAS
AF:
0.635
Gnomad SAS
AF:
0.245
Gnomad FIN
AF:
0.178
Gnomad MID
AF:
0.228
Gnomad NFE
AF:
0.195
Gnomad OTH
AF:
0.210
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.201
AC:
30575
AN:
152120
Hom.:
3773
Cov.:
32
AF XY:
0.205
AC XY:
15241
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.133
Gnomad4 AMR
AF:
0.253
Gnomad4 ASJ
AF:
0.273
Gnomad4 EAS
AF:
0.635
Gnomad4 SAS
AF:
0.246
Gnomad4 FIN
AF:
0.178
Gnomad4 NFE
AF:
0.195
Gnomad4 OTH
AF:
0.211
Alfa
AF:
0.210
Hom.:
8484
Bravo
AF:
0.206
Asia WGS
AF:
0.390
AC:
1355
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.27
CADD
Benign
15
DANN
Benign
0.80

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: rs2225614; hg19: chr9-24111280; COSMIC: COSV62761449; API