rs6841405

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 0.291 in 141,540 control chromosomes in the GnomAD database, including 6,672 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 0.29 ( 6672 hom., cov: 24)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.77
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=-1.02).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.383 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:
0.291
AC:
41189
AN:
141550
Hom.:
6671
Cov.:
24
show subpopulations
Gnomad AFR
AF:
0.153
Gnomad AMI
AF:
0.423
Gnomad AMR
AF:
0.389
Gnomad ASJ
AF:
0.240
Gnomad EAS
AF:
0.150
Gnomad SAS
AF:
0.398
Gnomad FIN
AF:
0.264
Gnomad MID
AF:
0.240
Gnomad NFE
AF:
0.359
Gnomad OTH
AF:
0.303
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.291
AC:
41195
AN:
141540
Hom.:
6672
Cov.:
24
AF XY:
0.290
AC XY:
19838
AN XY:
68402
show subpopulations
Gnomad4 AFR
AF:
0.154
Gnomad4 AMR
AF:
0.389
Gnomad4 ASJ
AF:
0.240
Gnomad4 EAS
AF:
0.149
Gnomad4 SAS
AF:
0.399
Gnomad4 FIN
AF:
0.264
Gnomad4 NFE
AF:
0.359
Gnomad4 OTH
AF:
0.302
Alfa
AF:
0.340
Hom.:
898

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.29
DANN
Benign
0.084

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: rs6841405; hg19: chr4-65067406; API