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GeneBe

rs17504636

Variant summary

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

The ENST00000612595.2(ENSG00000275016):​n.204+6057C>T 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 0.226 in 151,916 control chromosomes in the GnomAD database, including 3,987 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 0.23 ( 3987 hom., cov: 32)

Consequence


ENST00000612595.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.723
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=-0.54).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 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
ENST00000612595.2 linkuse as main transcriptn.204+6057C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.226
AC:
34281
AN:
151798
Hom.:
3978
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.238
Gnomad AMI
AF:
0.131
Gnomad AMR
AF:
0.253
Gnomad ASJ
AF:
0.202
Gnomad EAS
AF:
0.216
Gnomad SAS
AF:
0.292
Gnomad FIN
AF:
0.217
Gnomad MID
AF:
0.178
Gnomad NFE
AF:
0.212
Gnomad OTH
AF:
0.233
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.226
AC:
34316
AN:
151916
Hom.:
3987
Cov.:
32
AF XY:
0.225
AC XY:
16729
AN XY:
74236
show subpopulations
Gnomad4 AFR
AF:
0.238
Gnomad4 AMR
AF:
0.253
Gnomad4 ASJ
AF:
0.202
Gnomad4 EAS
AF:
0.215
Gnomad4 SAS
AF:
0.291
Gnomad4 FIN
AF:
0.217
Gnomad4 NFE
AF:
0.212
Gnomad4 OTH
AF:
0.240
Alfa
AF:
0.216
Hom.:
5250
Bravo
AF:
0.231
Asia WGS
AF:
0.290
AC:
1009
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
6.1
DANN
Benign
0.59

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: rs17504636; hg19: chr15-96187805; API