rs1908806

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 0.905 in 152,056 control chromosomes in the GnomAD database, including 62,724 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 0.91 ( 62724 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0280
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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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:
0.905
AC:
137532
AN:
151938
Hom.:
62680
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.777
Gnomad AMI
AF:
0.935
Gnomad AMR
AF:
0.944
Gnomad ASJ
AF:
0.954
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
0.980
Gnomad FIN
AF:
0.969
Gnomad MID
AF:
0.914
Gnomad NFE
AF:
0.949
Gnomad OTH
AF:
0.910
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.905
AC:
137633
AN:
152056
Hom.:
62724
Cov.:
32
AF XY:
0.910
AC XY:
67636
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.777
Gnomad4 AMR
AF:
0.945
Gnomad4 ASJ
AF:
0.954
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
0.981
Gnomad4 FIN
AF:
0.969
Gnomad4 NFE
AF:
0.949
Gnomad4 OTH
AF:
0.911
Alfa
AF:
0.926
Hom.:
8139
Bravo
AF:
0.896
Asia WGS
AF:
0.978
AC:
3395
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
8.1
DANN
Benign
0.73

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: rs1908806; hg19: chr4-44964953; API