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GeneBe

rs1026374

chr8-2797033-C-Achr8-2797033-C-Gchr8-2797033-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NR_168443.1(LOC105377785):n.539-7553C>A 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 0.00821 in 152,040 control chromosomes in the GnomAD database, including 17 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 0.0082 ( 17 hom., cov: 31)

Consequence

LOC105377785
NR_168443.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37
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=-1.0).
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00821 (1249/152040) while in subpopulation AFR AF= 0.0247 (1022/41454). AF 95% confidence interval is 0.0234. There are 17 homozygotes in gnomad4. There are 609 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 17 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105377785NR_168443.1 linkuse as main transcriptn.539-7553C>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000654515.1 linkuse as main transcriptn.532-7553C>A intron_variant, non_coding_transcript_variant
ENST00000520024.1 linkuse as main transcriptn.177-7553C>A intron_variant, non_coding_transcript_variant 3
ENST00000662575.1 linkuse as main transcriptn.81+1658C>A intron_variant, non_coding_transcript_variant
ENST00000670600.1 linkuse as main transcriptn.539-7553C>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00821
AC:
1247
AN:
151926
Hom.:
17
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0247
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00917
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0159
Gnomad NFE
AF:
0.000956
Gnomad OTH
AF:
0.00813
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:
0.00821
AC:
1249
AN:
152040
Hom.:
17
Cov.:
31
AF XY:
0.00819
AC XY:
609
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.0247
Gnomad4 AMR
AF:
0.00916
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000956
Gnomad4 OTH
AF:
0.00805
Alfa
AF:
0.0000696
Hom.:
2618

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
Cadd
Benign
0.21
Dann
Benign
0.48

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: rs1026374; hg19: chr8-2654569; API