1-27401536-A-G

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 0.0858 in 152,230 control chromosomes in the GnomAD database, including 1,856 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 0.086 ( 1856 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.261
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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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:
0.0857
AC:
13030
AN:
152112
Hom.:
1850
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.295
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0374
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00165
Gnomad FIN
AF:
0.000659
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.00147
Gnomad OTH
AF:
0.0674
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0858
AC:
13068
AN:
152230
Hom.:
1856
Cov.:
33
AF XY:
0.0827
AC XY:
6153
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.295
Gnomad4 AMR
AF:
0.0372
Gnomad4 ASJ
AF:
0.00173
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00166
Gnomad4 FIN
AF:
0.000659
Gnomad4 NFE
AF:
0.00147
Gnomad4 OTH
AF:
0.0672
Alfa
AF:
0.0539
Hom.:
235
Bravo
AF:
0.0993
Asia WGS
AF:
0.0200
AC:
72
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
6.5
DANN
Benign
0.82

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: rs7516721; hg19: chr1-27728040; API