rs7600259

Variant summary

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

The ENST00000453451.5(ENSG00000226994):​n.180+36734T>G 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 0.121 in 152,192 control chromosomes in the GnomAD database, including 1,119 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 0.12 ( 1119 hom., cov: 32)

Consequence


ENST00000453451.5 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.73
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=-0.51).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000453451.5 linkuse as main transcriptn.180+36734T>G intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.121
AC:
18468
AN:
152074
Hom.:
1117
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.132
Gnomad AMI
AF:
0.101
Gnomad AMR
AF:
0.0923
Gnomad ASJ
AF:
0.179
Gnomad EAS
AF:
0.117
Gnomad SAS
AF:
0.113
Gnomad FIN
AF:
0.111
Gnomad MID
AF:
0.136
Gnomad NFE
AF:
0.121
Gnomad OTH
AF:
0.119
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.121
AC:
18478
AN:
152192
Hom.:
1119
Cov.:
32
AF XY:
0.120
AC XY:
8900
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.132
Gnomad4 AMR
AF:
0.0922
Gnomad4 ASJ
AF:
0.179
Gnomad4 EAS
AF:
0.117
Gnomad4 SAS
AF:
0.112
Gnomad4 FIN
AF:
0.111
Gnomad4 NFE
AF:
0.121
Gnomad4 OTH
AF:
0.119
Alfa
AF:
0.123
Hom.:
2436
Bravo
AF:
0.121
Asia WGS
AF:
0.108
AC:
375
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
CADD
Benign
17
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: rs7600259; hg19: chr2-35093293; API