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GeneBe

rs2568958

chr1-72299433-G-Achr1-72299433-G-Cchr1-72299433-G-T

Variant summary

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

The ENST00000665984.1(ENSG00000286863):n.153+16028G>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 0.625 in 151,952 control chromosomes in the GnomAD database, including 30,286 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 0.62 ( 30286 hom., cov: 31)

Consequence


ENST00000665984.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.388
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=-0.95).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105378797XR_001737670.2 linkuse as main transcriptn.472+16028G>A intron_variant, non_coding_transcript_variant
LOC105378797XR_001737671.3 linkuse as main transcriptn.472+16028G>A intron_variant, non_coding_transcript_variant
LOC105378797XR_947505.3 linkuse as main transcriptn.472+16028G>A intron_variant, non_coding_transcript_variant
LOC105378797XR_947506.3 linkuse as main transcriptn.472+16028G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000665984.1 linkuse as main transcriptn.153+16028G>A intron_variant, non_coding_transcript_variant
ENST00000653965.1 linkuse as main transcriptn.236+16028G>A intron_variant, non_coding_transcript_variant
ENST00000667836.1 linkuse as main transcriptn.227+16028G>A intron_variant, non_coding_transcript_variant
ENST00000688733.1 linkuse as main transcriptn.56+16028G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.625
AC:
94872
AN:
151834
Hom.:
30272
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.541
Gnomad AMI
AF:
0.554
Gnomad AMR
AF:
0.708
Gnomad ASJ
AF:
0.735
Gnomad EAS
AF:
0.924
Gnomad SAS
AF:
0.667
Gnomad FIN
AF:
0.648
Gnomad MID
AF:
0.722
Gnomad NFE
AF:
0.623
Gnomad OTH
AF:
0.640
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:
0.625
AC:
94918
AN:
151952
Hom.:
30286
Cov.:
31
AF XY:
0.631
AC XY:
46868
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.540
Gnomad4 AMR
AF:
0.708
Gnomad4 ASJ
AF:
0.735
Gnomad4 EAS
AF:
0.923
Gnomad4 SAS
AF:
0.668
Gnomad4 FIN
AF:
0.648
Gnomad4 NFE
AF:
0.623
Gnomad4 OTH
AF:
0.643
Alfa
AF:
0.638
Hom.:
66558
Bravo
AF:
0.628
Asia WGS
AF:
0.753
AC:
2614
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
Cadd
Benign
0.14
Dann
Benign
0.31

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: rs2568958; hg19: chr1-72765116; API