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GeneBe

rs10517377

Positions:

Variant summary

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

The NR_122079.1(LOC439933):​n.361-5557A>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 0.18 in 152,214 control chromosomes in the GnomAD database, including 2,993 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 ( 2993 hom., cov: 32)

Consequence

LOC439933
NR_122079.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.33
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC439933NR_122079.1 linkuse as main transcriptn.361-5557A>C intron_variant, non_coding_transcript_variant
LOC439933NR_122080.1 linkuse as main transcriptn.338-5845A>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000499292.2 linkuse as main transcriptn.361-5557A>C intron_variant, non_coding_transcript_variant 1
ENST00000502245.2 linkuse as main transcriptn.386-5845A>C intron_variant, non_coding_transcript_variant 1
ENST00000691596.1 linkuse as main transcriptn.193-5845A>C intron_variant, non_coding_transcript_variant
ENST00000692213.1 linkuse as main transcriptn.193-5557A>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.180
AC:
27428
AN:
152096
Hom.:
2992
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0674
Gnomad AMI
AF:
0.377
Gnomad AMR
AF:
0.223
Gnomad ASJ
AF:
0.325
Gnomad EAS
AF:
0.0758
Gnomad SAS
AF:
0.235
Gnomad FIN
AF:
0.153
Gnomad MID
AF:
0.218
Gnomad NFE
AF:
0.237
Gnomad OTH
AF:
0.194
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.180
AC:
27428
AN:
152214
Hom.:
2993
Cov.:
32
AF XY:
0.178
AC XY:
13241
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.0673
Gnomad4 AMR
AF:
0.223
Gnomad4 ASJ
AF:
0.325
Gnomad4 EAS
AF:
0.0762
Gnomad4 SAS
AF:
0.236
Gnomad4 FIN
AF:
0.153
Gnomad4 NFE
AF:
0.237
Gnomad4 OTH
AF:
0.191
Alfa
AF:
0.130
Hom.:
292
Bravo
AF:
0.176
Asia WGS
AF:
0.141
AC:
495
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.28
DANN
Benign
0.56

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: rs10517377; hg19: chr4-36269012; API