rs1330320

Variant summary

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

The variant allele was found at a frequency of 0.4 in 151,908 control chromosomes in the GnomAD database, including 12,295 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 0.40 ( 12295 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.694
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.400
AC:
60707
AN:
151790
Hom.:
12281
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.409
Gnomad AMI
AF:
0.375
Gnomad AMR
AF:
0.420
Gnomad ASJ
AF:
0.370
Gnomad EAS
AF:
0.513
Gnomad SAS
AF:
0.318
Gnomad FIN
AF:
0.377
Gnomad MID
AF:
0.354
Gnomad NFE
AF:
0.393
Gnomad OTH
AF:
0.393
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.400
AC:
60764
AN:
151908
Hom.:
12295
Cov.:
31
AF XY:
0.399
AC XY:
29637
AN XY:
74256
show subpopulations
Gnomad4 AFR
AF:
0.409
Gnomad4 AMR
AF:
0.420
Gnomad4 ASJ
AF:
0.370
Gnomad4 EAS
AF:
0.513
Gnomad4 SAS
AF:
0.320
Gnomad4 FIN
AF:
0.377
Gnomad4 NFE
AF:
0.393
Gnomad4 OTH
AF:
0.391
Alfa
AF:
0.393
Hom.:
24186
Bravo
AF:
0.405
Asia WGS
AF:
0.403
AC:
1402
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.51
DANN
Benign
0.74

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: rs1330320; hg19: chr9-21255150; COSMIC: COSV69450713; API