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GeneBe

rs2872507

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 0.389 in 152,006 control chromosomes in the GnomAD database, including 12,248 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 0.39 ( 12248 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.354
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=-1.06).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 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:
0.389
AC:
59125
AN:
151888
Hom.:
12236
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.260
Gnomad AMI
AF:
0.661
Gnomad AMR
AF:
0.390
Gnomad ASJ
AF:
0.416
Gnomad EAS
AF:
0.270
Gnomad SAS
AF:
0.370
Gnomad FIN
AF:
0.532
Gnomad MID
AF:
0.361
Gnomad NFE
AF:
0.452
Gnomad OTH
AF:
0.376
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.389
AC:
59173
AN:
152006
Hom.:
12248
Cov.:
32
AF XY:
0.392
AC XY:
29125
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.261
Gnomad4 AMR
AF:
0.391
Gnomad4 ASJ
AF:
0.416
Gnomad4 EAS
AF:
0.270
Gnomad4 SAS
AF:
0.371
Gnomad4 FIN
AF:
0.532
Gnomad4 NFE
AF:
0.452
Gnomad4 OTH
AF:
0.374
Alfa
AF:
0.433
Hom.:
31821
Bravo
AF:
0.367
Asia WGS
AF:
0.370
AC:
1286
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
Cadd
Benign
1.0
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: rs2872507; hg19: chr17-38040763; API