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GeneBe

rs2602629

Variant summary

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

The ENST00000707165.1(ENSG00000291325):n.260-30501G>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 0.58 in 152,030 control chromosomes in the GnomAD database, including 26,822 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 0.58 ( 26822 hom., cov: 32)

Consequence


ENST00000707165.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.108
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
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000707165.1 linkuse as main transcriptn.260-30501G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.580
AC:
88099
AN:
151912
Hom.:
26786
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.753
Gnomad AMI
AF:
0.383
Gnomad AMR
AF:
0.475
Gnomad ASJ
AF:
0.619
Gnomad EAS
AF:
0.751
Gnomad SAS
AF:
0.761
Gnomad FIN
AF:
0.490
Gnomad MID
AF:
0.563
Gnomad NFE
AF:
0.488
Gnomad OTH
AF:
0.535
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.580
AC:
88200
AN:
152030
Hom.:
26822
Cov.:
32
AF XY:
0.584
AC XY:
43365
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.753
Gnomad4 AMR
AF:
0.475
Gnomad4 ASJ
AF:
0.619
Gnomad4 EAS
AF:
0.751
Gnomad4 SAS
AF:
0.760
Gnomad4 FIN
AF:
0.490
Gnomad4 NFE
AF:
0.488
Gnomad4 OTH
AF:
0.540
Alfa
AF:
0.508
Hom.:
30241
Bravo
AF:
0.580
Asia WGS
AF:
0.760
AC:
2641
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
3.1
Dann
Benign
0.68

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: rs2602629; hg19: chr2-4456055; COSMIC: COSV50574091; API