rs222541

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 0.489 in 151,520 control chromosomes in the GnomAD database, including 22,110 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 0.49 ( 22110 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.747
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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:
0.488
AC:
73938
AN:
151402
Hom.:
22052
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.844
Gnomad AMI
AF:
0.452
Gnomad AMR
AF:
0.322
Gnomad ASJ
AF:
0.436
Gnomad EAS
AF:
0.567
Gnomad SAS
AF:
0.536
Gnomad FIN
AF:
0.318
Gnomad MID
AF:
0.551
Gnomad NFE
AF:
0.330
Gnomad OTH
AF:
0.455
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.489
AC:
74037
AN:
151520
Hom.:
22110
Cov.:
32
AF XY:
0.489
AC XY:
36206
AN XY:
74054
show subpopulations
Gnomad4 AFR
AF:
0.844
Gnomad4 AMR
AF:
0.321
Gnomad4 ASJ
AF:
0.436
Gnomad4 EAS
AF:
0.567
Gnomad4 SAS
AF:
0.535
Gnomad4 FIN
AF:
0.318
Gnomad4 NFE
AF:
0.330
Gnomad4 OTH
AF:
0.454
Alfa
AF:
0.278
Hom.:
775
Bravo
AF:
0.502
Asia WGS
AF:
0.588
AC:
2044
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.8
DANN
Benign
0.68

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: rs222541; hg19: chr6-95231163; API