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 rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein 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