rs7201071

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 0.0954 in 152,066 control chromosomes in the GnomAD database, including 1,383 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 0.095 ( 1383 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04
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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0952
AC:
14461
AN:
151950
Hom.:
1375
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.244
Gnomad AMI
AF:
0.0749
Gnomad AMR
AF:
0.0835
Gnomad ASJ
AF:
0.0576
Gnomad EAS
AF:
0.0541
Gnomad SAS
AF:
0.0422
Gnomad FIN
AF:
0.0278
Gnomad MID
AF:
0.0665
Gnomad NFE
AF:
0.0272
Gnomad OTH
AF:
0.0955
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0954
AC:
14501
AN:
152066
Hom.:
1383
Cov.:
31
AF XY:
0.0931
AC XY:
6923
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.244
Gnomad4 AMR
AF:
0.0843
Gnomad4 ASJ
AF:
0.0576
Gnomad4 EAS
AF:
0.0536
Gnomad4 SAS
AF:
0.0424
Gnomad4 FIN
AF:
0.0278
Gnomad4 NFE
AF:
0.0272
Gnomad4 OTH
AF:
0.0945
Alfa
AF:
0.0631
Hom.:
239
Bravo
AF:
0.107
Asia WGS
AF:
0.0580
AC:
203
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
0.094
DANN
Benign
0.38

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: rs7201071; hg19: chr16-51993405; API