rs2201806

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 0.383 in 151,960 control chromosomes in the GnomAD database, including 11,713 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 0.38 ( 11713 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.627
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=-1.0).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.518 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:
0.383
AC:
58204
AN:
151842
Hom.:
11703
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.266
Gnomad AMI
AF:
0.505
Gnomad AMR
AF:
0.527
Gnomad ASJ
AF:
0.323
Gnomad EAS
AF:
0.400
Gnomad SAS
AF:
0.462
Gnomad FIN
AF:
0.388
Gnomad MID
AF:
0.367
Gnomad NFE
AF:
0.417
Gnomad OTH
AF:
0.373
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.383
AC:
58246
AN:
151960
Hom.:
11713
Cov.:
32
AF XY:
0.384
AC XY:
28537
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.266
Gnomad4 AMR
AF:
0.527
Gnomad4 ASJ
AF:
0.323
Gnomad4 EAS
AF:
0.400
Gnomad4 SAS
AF:
0.463
Gnomad4 FIN
AF:
0.388
Gnomad4 NFE
AF:
0.417
Gnomad4 OTH
AF:
0.376
Alfa
AF:
0.412
Hom.:
2079
Bravo
AF:
0.390
Asia WGS
AF:
0.432
AC:
1499
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.1
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: rs2201806; hg19: chr6-164982150; COSMIC: COSV69432953; API