rs1919796

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 0.272 in 152,010 control chromosomes in the GnomAD database, including 7,842 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 0.27 ( 7842 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.330
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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 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:
0.272
AC:
41312
AN:
151892
Hom.:
7823
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.516
Gnomad AMI
AF:
0.0980
Gnomad AMR
AF:
0.281
Gnomad ASJ
AF:
0.132
Gnomad EAS
AF:
0.468
Gnomad SAS
AF:
0.156
Gnomad FIN
AF:
0.183
Gnomad MID
AF:
0.168
Gnomad NFE
AF:
0.139
Gnomad OTH
AF:
0.261
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.272
AC:
41379
AN:
152010
Hom.:
7842
Cov.:
33
AF XY:
0.274
AC XY:
20370
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.516
Gnomad4 AMR
AF:
0.281
Gnomad4 ASJ
AF:
0.132
Gnomad4 EAS
AF:
0.467
Gnomad4 SAS
AF:
0.156
Gnomad4 FIN
AF:
0.183
Gnomad4 NFE
AF:
0.139
Gnomad4 OTH
AF:
0.264
Alfa
AF:
0.161
Hom.:
4904
Bravo
AF:
0.294
Asia WGS
AF:
0.333
AC:
1156
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.17
DANN
Benign
0.35

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: rs1919796; hg19: chr7-9323220; API