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GeneBe

rs2394075

chr10-64521033-T-A

Variant summary

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

The ENST00000654191.1(ENSG00000228566):n.734-170409T>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 0.527 in 151,822 control chromosomes in the GnomAD database, including 21,871 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 0.53 ( 21871 hom., cov: 30)

Consequence


ENST00000654191.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.130
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 = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124902439XR_007062161.1 linkuse as main transcriptn.715-170409T>A intron_variant, non_coding_transcript_variant
LOC124902439XR_007062160.1 linkuse as main transcriptn.713-170409T>A intron_variant, non_coding_transcript_variant
LOC124902439XR_007062165.1 linkuse as main transcriptn.270-170409T>A intron_variant, non_coding_transcript_variant
LOC124902439XR_007062166.1 linkuse as main transcriptn.433-170409T>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000654191.1 linkuse as main transcriptn.734-170409T>A intron_variant, non_coding_transcript_variant
ENST00000660795.1 linkuse as main transcriptn.580-170409T>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.528
AC:
80026
AN:
151702
Hom.:
21858
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.566
Gnomad AMI
AF:
0.542
Gnomad AMR
AF:
0.423
Gnomad ASJ
AF:
0.464
Gnomad EAS
AF:
0.0729
Gnomad SAS
AF:
0.387
Gnomad FIN
AF:
0.566
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.570
Gnomad OTH
AF:
0.506
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:
0.527
AC:
80067
AN:
151822
Hom.:
21871
Cov.:
30
AF XY:
0.520
AC XY:
38556
AN XY:
74180
show subpopulations
Gnomad4 AFR
AF:
0.566
Gnomad4 AMR
AF:
0.423
Gnomad4 ASJ
AF:
0.464
Gnomad4 EAS
AF:
0.0731
Gnomad4 SAS
AF:
0.389
Gnomad4 FIN
AF:
0.566
Gnomad4 NFE
AF:
0.570
Gnomad4 OTH
AF:
0.499
Alfa
AF:
0.563
Hom.:
3031
Bravo
AF:
0.516
Asia WGS
AF:
0.243
AC:
847
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
2.3
Dann
Benign
0.79

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: rs2394075; hg19: chr10-66280790; API