rs1441835

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 0.144 in 152,118 control chromosomes in the GnomAD database, including 3,305 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 0.14 ( 3305 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.112
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=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 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:
0.144
AC:
21855
AN:
152000
Hom.:
3288
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.386
Gnomad AMI
AF:
0.0198
Gnomad AMR
AF:
0.0578
Gnomad ASJ
AF:
0.00894
Gnomad EAS
AF:
0.121
Gnomad SAS
AF:
0.0863
Gnomad FIN
AF:
0.0651
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.0441
Gnomad OTH
AF:
0.103
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.144
AC:
21911
AN:
152118
Hom.:
3305
Cov.:
32
AF XY:
0.144
AC XY:
10682
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.387
Gnomad4 AMR
AF:
0.0575
Gnomad4 ASJ
AF:
0.00894
Gnomad4 EAS
AF:
0.121
Gnomad4 SAS
AF:
0.0856
Gnomad4 FIN
AF:
0.0651
Gnomad4 NFE
AF:
0.0441
Gnomad4 OTH
AF:
0.102
Alfa
AF:
0.101
Hom.:
244
Bravo
AF:
0.156

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
5.3
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: rs1441835; hg19: chr1-30172635; API