rs9600764

Variant summary

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

The ENST00000648060.1(ENSG00000285572):​n.230-7148T>C 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 0.068 in 152,232 control chromosomes in the GnomAD database, including 610 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 0.068 ( 610 hom., cov: 32)

Consequence


ENST00000648060.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.852
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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC105370265XR_001749923.2 linkuse as main transcriptn.118-7148T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000648060.1 linkuse as main transcriptn.230-7148T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0679
AC:
10322
AN:
152114
Hom.:
607
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.162
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.0450
Gnomad ASJ
AF:
0.0619
Gnomad EAS
AF:
0.00308
Gnomad SAS
AF:
0.0116
Gnomad FIN
AF:
0.00669
Gnomad MID
AF:
0.0823
Gnomad NFE
AF:
0.0353
Gnomad OTH
AF:
0.0590
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0680
AC:
10354
AN:
152232
Hom.:
610
Cov.:
32
AF XY:
0.0649
AC XY:
4828
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.163
Gnomad4 AMR
AF:
0.0450
Gnomad4 ASJ
AF:
0.0619
Gnomad4 EAS
AF:
0.00309
Gnomad4 SAS
AF:
0.0116
Gnomad4 FIN
AF:
0.00669
Gnomad4 NFE
AF:
0.0353
Gnomad4 OTH
AF:
0.0598
Alfa
AF:
0.0430
Hom.:
257
Bravo
AF:
0.0745
Asia WGS
AF:
0.0330
AC:
116
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.37
DANN
Benign
0.77

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: rs9600764; hg19: chr13-77310793; API