rs649446

Variant summary

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

The ENST00000660751.1(ENSG00000287425):​n.1352C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,146 control chromosomes in the GnomAD database, including 3,699 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 0.22 ( 3699 hom., cov: 32)

Consequence


ENST00000660751.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.695
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=-0.68).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 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
ENST00000660751.1 linkuse as main transcriptn.1352C>T non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.216
AC:
32879
AN:
152026
Hom.:
3699
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.269
Gnomad AMI
AF:
0.162
Gnomad AMR
AF:
0.174
Gnomad ASJ
AF:
0.212
Gnomad EAS
AF:
0.285
Gnomad SAS
AF:
0.235
Gnomad FIN
AF:
0.206
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.190
Gnomad OTH
AF:
0.214
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.216
AC:
32899
AN:
152146
Hom.:
3699
Cov.:
32
AF XY:
0.218
AC XY:
16200
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.269
Gnomad4 AMR
AF:
0.174
Gnomad4 ASJ
AF:
0.212
Gnomad4 EAS
AF:
0.285
Gnomad4 SAS
AF:
0.234
Gnomad4 FIN
AF:
0.206
Gnomad4 NFE
AF:
0.190
Gnomad4 OTH
AF:
0.212
Alfa
AF:
0.212
Hom.:
417
Bravo
AF:
0.215
Asia WGS
AF:
0.239
AC:
831
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
3.6
DANN
Benign
0.80

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: rs649446; hg19: chr11-73695845; API