rs72844458

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The variant allele was found at a frequency of 0.0357 in 152,288 control chromosomes in the GnomAD database, including 139 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 0.036 ( 139 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.649
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=-0.84).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0357 (5435/152288) while in subpopulation NFE AF= 0.0459 (3120/68026). AF 95% confidence interval is 0.0445. There are 139 homozygotes in gnomad4. There are 2861 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 139 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0357
AC:
5434
AN:
152170
Hom.:
138
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00859
Gnomad AMI
AF:
0.0198
Gnomad AMR
AF:
0.0367
Gnomad ASJ
AF:
0.0369
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00931
Gnomad FIN
AF:
0.105
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.0459
Gnomad OTH
AF:
0.0378
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0357
AC:
5435
AN:
152288
Hom.:
139
Cov.:
33
AF XY:
0.0384
AC XY:
2861
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.00856
Gnomad4 AMR
AF:
0.0367
Gnomad4 ASJ
AF:
0.0369
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00932
Gnomad4 FIN
AF:
0.105
Gnomad4 NFE
AF:
0.0459
Gnomad4 OTH
AF:
0.0374
Alfa
AF:
0.0376
Hom.:
11
Bravo
AF:
0.0293
Asia WGS
AF:
0.00577
AC:
22
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
1.8
DANN
Benign
0.70

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: rs72844458; hg19: chr2-85764027; API