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GeneBe

rs9977499

Positions:

Variant summary

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

The XR_007067831.1(LOC124905003):​n.1855G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,008 control chromosomes in the GnomAD database, including 18,567 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 0.47 ( 18567 hom., cov: 32)
Failed GnomAD Quality Control

Consequence

LOC124905003
XR_007067831.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33
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
?
    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=-0.94).
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 = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124905003XR_007067831.1 linkuse as main transcriptn.1855G>A non_coding_transcript_exon_variant 1/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000420186.2 linkuse as main transcriptn.332-1522G>A intron_variant, non_coding_transcript_variant 1
ENST00000447384.1 linkuse as main transcriptn.291-35C>T intron_variant, non_coding_transcript_variant 1
ENST00000666822.1 linkuse as main transcriptn.299-35C>T intron_variant, non_coding_transcript_variant
ENST00000656258.1 linkuse as main transcriptn.334-35C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.468
AC:
71079
AN:
151890
Hom.:
18548
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.252
Gnomad AMI
AF:
0.535
Gnomad AMR
AF:
0.461
Gnomad ASJ
AF:
0.502
Gnomad EAS
AF:
0.191
Gnomad SAS
AF:
0.569
Gnomad FIN
AF:
0.495
Gnomad MID
AF:
0.408
Gnomad NFE
AF:
0.608
Gnomad OTH
AF:
0.467
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.468
AC:
71115
AN:
152008
Hom.:
18567
Cov.:
32
AF XY:
0.462
AC XY:
34344
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.252
Gnomad4 AMR
AF:
0.461
Gnomad4 ASJ
AF:
0.502
Gnomad4 EAS
AF:
0.190
Gnomad4 SAS
AF:
0.571
Gnomad4 FIN
AF:
0.495
Gnomad4 NFE
AF:
0.608
Gnomad4 OTH
AF:
0.471
Alfa
AF:
0.565
Hom.:
30188
Bravo
AF:
0.448
Asia WGS
AF:
0.352
AC:
1226
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.56
DANN
Benign
0.78

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: rs9977499; hg19: chr21-28734997; API