rs346923

Variant summary

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

The ENST00000660768.1(ENSG00000287999):​n.102+5510C>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 0.201 in 152,066 control chromosomes in the GnomAD database, including 4,436 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 0.20 ( 4436 hom., cov: 32)

Consequence


ENST00000660768.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03
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=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 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
ENST00000660768.1 linkuse as main transcriptn.102+5510C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.201
AC:
30548
AN:
151948
Hom.:
4413
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.415
Gnomad AMI
AF:
0.111
Gnomad AMR
AF:
0.135
Gnomad ASJ
AF:
0.182
Gnomad EAS
AF:
0.206
Gnomad SAS
AF:
0.133
Gnomad FIN
AF:
0.0799
Gnomad MID
AF:
0.168
Gnomad NFE
AF:
0.111
Gnomad OTH
AF:
0.192
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.201
AC:
30626
AN:
152066
Hom.:
4436
Cov.:
32
AF XY:
0.197
AC XY:
14635
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.416
Gnomad4 AMR
AF:
0.135
Gnomad4 ASJ
AF:
0.182
Gnomad4 EAS
AF:
0.206
Gnomad4 SAS
AF:
0.133
Gnomad4 FIN
AF:
0.0799
Gnomad4 NFE
AF:
0.112
Gnomad4 OTH
AF:
0.196
Alfa
AF:
0.130
Hom.:
2449
Bravo
AF:
0.216
Asia WGS
AF:
0.191
AC:
665
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
8.7
DANN
Benign
0.75

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: rs346923; hg19: chr4-53412129; API