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GeneBe

rs1979406

Variant summary

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

The NR_110817.1(LOC101928135):n.207-118364A>G 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 0.117 in 152,170 control chromosomes in the GnomAD database, including 1,288 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 ( 1288 hom., cov: 32)

Consequence

LOC101928135
NR_110817.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.848
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC101928135NR_110817.1 linkuse as main transcriptn.207-118364A>G intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.117
AC:
17840
AN:
152052
Hom.:
1288
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.208
Gnomad AMI
AF:
0.0779
Gnomad AMR
AF:
0.0815
Gnomad ASJ
AF:
0.0574
Gnomad EAS
AF:
0.0985
Gnomad SAS
AF:
0.0978
Gnomad FIN
AF:
0.0756
Gnomad MID
AF:
0.0443
Gnomad NFE
AF:
0.0834
Gnomad OTH
AF:
0.111
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.117
AC:
17870
AN:
152170
Hom.:
1288
Cov.:
32
AF XY:
0.116
AC XY:
8638
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.208
Gnomad4 AMR
AF:
0.0813
Gnomad4 ASJ
AF:
0.0574
Gnomad4 EAS
AF:
0.0983
Gnomad4 SAS
AF:
0.0981
Gnomad4 FIN
AF:
0.0756
Gnomad4 NFE
AF:
0.0834
Gnomad4 OTH
AF:
0.114
Alfa
AF:
0.104
Hom.:
144
Bravo
AF:
0.123
Asia WGS
AF:
0.112
AC:
387
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
1.8
Dann
Benign
0.74

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: rs1979406; hg19: chr3-35039322; API