GeneBe

rs3037354

Positions:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XR_001745132.2(LOC107986777):​n.209+36049_209+36050del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 6174 hom., cov: 19)

Consequence

LOC107986777
XR_001745132.2 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.796
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 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+36049_209+36050del intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.281
AC:
42663
AN:
151926
Hom.:
6166
Cov.:
19
show subpopulations
Gnomad AFR
AF:
0.343
Gnomad AMI
AF:
0.403
Gnomad AMR
AF:
0.223
Gnomad ASJ
AF:
0.245
Gnomad EAS
AF:
0.308
Gnomad SAS
AF:
0.298
Gnomad FIN
AF:
0.251
Gnomad MID
AF:
0.303
Gnomad NFE
AF:
0.257
Gnomad OTH
AF:
0.285
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.281
AC:
42692
AN:
152044
Hom.:
6174
Cov.:
19
AF XY:
0.280
AC XY:
20794
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.343
Gnomad4 AMR
AF:
0.223
Gnomad4 ASJ
AF:
0.245
Gnomad4 EAS
AF:
0.309
Gnomad4 SAS
AF:
0.298
Gnomad4 FIN
AF:
0.251
Gnomad4 NFE
AF:
0.257
Gnomad4 OTH
AF:
0.285
Alfa
AF:
0.268
Hom.:
710
Bravo
AF:
0.281
Asia WGS
AF:
0.310
AC:
1076
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs3037354; hg19: chr7-24322925; API