rs12700524

Variant summary

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

The XR_001745132.2(LOC107986777):​n.209+37562T>C 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 0.123 in 152,264 control chromosomes in the GnomAD database, including 1,201 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 0.12 ( 1201 hom., cov: 32)

Consequence

LOC107986777
XR_001745132.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38
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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC107986777XR_001745132.2 linkuse as main transcriptn.209+37562T>C intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.123
AC:
18691
AN:
152146
Hom.:
1201
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.109
Gnomad AMI
AF:
0.112
Gnomad AMR
AF:
0.105
Gnomad ASJ
AF:
0.155
Gnomad EAS
AF:
0.0131
Gnomad SAS
AF:
0.0743
Gnomad FIN
AF:
0.117
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.146
Gnomad OTH
AF:
0.128
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.123
AC:
18702
AN:
152264
Hom.:
1201
Cov.:
32
AF XY:
0.120
AC XY:
8923
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.109
Gnomad4 AMR
AF:
0.104
Gnomad4 ASJ
AF:
0.155
Gnomad4 EAS
AF:
0.0131
Gnomad4 SAS
AF:
0.0746
Gnomad4 FIN
AF:
0.117
Gnomad4 NFE
AF:
0.147
Gnomad4 OTH
AF:
0.126
Alfa
AF:
0.138
Hom.:
804
Bravo
AF:
0.123
Asia WGS
AF:
0.0640
AC:
225
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.0090
DANN
Benign
0.49

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: rs12700524; hg19: chr7-24321414; API