rs1948522

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 0.166 in 152,110 control chromosomes in the GnomAD database, including 2,369 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 0.17 ( 2369 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.282
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=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 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

Frequencies

GnomAD3 genomes
AF:
0.166
AC:
25291
AN:
151994
Hom.:
2367
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0899
Gnomad AMI
AF:
0.225
Gnomad AMR
AF:
0.147
Gnomad ASJ
AF:
0.138
Gnomad EAS
AF:
0.116
Gnomad SAS
AF:
0.122
Gnomad FIN
AF:
0.240
Gnomad MID
AF:
0.168
Gnomad NFE
AF:
0.213
Gnomad OTH
AF:
0.178
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.166
AC:
25296
AN:
152110
Hom.:
2369
Cov.:
32
AF XY:
0.165
AC XY:
12277
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.0897
Gnomad4 AMR
AF:
0.147
Gnomad4 ASJ
AF:
0.138
Gnomad4 EAS
AF:
0.115
Gnomad4 SAS
AF:
0.122
Gnomad4 FIN
AF:
0.240
Gnomad4 NFE
AF:
0.213
Gnomad4 OTH
AF:
0.181
Alfa
AF:
0.204
Hom.:
4760
Bravo
AF:
0.157
Asia WGS
AF:
0.134
AC:
466
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
3.5
DANN
Benign
0.29

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: rs1948522; hg19: chr9-27575785; API