rs12032381

Variant summary

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

The XR_922621.2(LOC105372932):​n.623-26408A>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 0.193 in 151,822 control chromosomes in the GnomAD database, including 3,368 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 0.19 ( 3368 hom., cov: 32)

Consequence

LOC105372932
XR_922621.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.264
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 (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105372932XR_922621.2 linkuse as main transcriptn.623-26408A>C intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.193
AC:
29331
AN:
151704
Hom.:
3366
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0624
Gnomad AMI
AF:
0.106
Gnomad AMR
AF:
0.241
Gnomad ASJ
AF:
0.217
Gnomad EAS
AF:
0.346
Gnomad SAS
AF:
0.228
Gnomad FIN
AF:
0.284
Gnomad MID
AF:
0.174
Gnomad NFE
AF:
0.234
Gnomad OTH
AF:
0.199
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.193
AC:
29339
AN:
151822
Hom.:
3368
Cov.:
32
AF XY:
0.198
AC XY:
14697
AN XY:
74178
show subpopulations
Gnomad4 AFR
AF:
0.0622
Gnomad4 AMR
AF:
0.241
Gnomad4 ASJ
AF:
0.217
Gnomad4 EAS
AF:
0.346
Gnomad4 SAS
AF:
0.228
Gnomad4 FIN
AF:
0.284
Gnomad4 NFE
AF:
0.234
Gnomad4 OTH
AF:
0.203
Alfa
AF:
0.226
Hom.:
1688
Bravo
AF:
0.185
Asia WGS
AF:
0.289
AC:
1004
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
0.38
DANN
Benign
0.21

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: rs12032381; hg19: chr1-221617076; API