rs2758886

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 0.232 in 151,894 control chromosomes in the GnomAD database, including 4,567 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 0.23 ( 4567 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.854
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=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 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:
0.232
AC:
35185
AN:
151778
Hom.:
4564
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.165
Gnomad AMI
AF:
0.323
Gnomad AMR
AF:
0.235
Gnomad ASJ
AF:
0.240
Gnomad EAS
AF:
0.00620
Gnomad SAS
AF:
0.120
Gnomad FIN
AF:
0.228
Gnomad MID
AF:
0.323
Gnomad NFE
AF:
0.295
Gnomad OTH
AF:
0.245
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.232
AC:
35200
AN:
151894
Hom.:
4567
Cov.:
32
AF XY:
0.226
AC XY:
16760
AN XY:
74248
show subpopulations
Gnomad4 AFR
AF:
0.165
Gnomad4 AMR
AF:
0.235
Gnomad4 ASJ
AF:
0.240
Gnomad4 EAS
AF:
0.00622
Gnomad4 SAS
AF:
0.122
Gnomad4 FIN
AF:
0.228
Gnomad4 NFE
AF:
0.295
Gnomad4 OTH
AF:
0.242
Alfa
AF:
0.268
Hom.:
1541
Bravo
AF:
0.231
Asia WGS
AF:
0.0630
AC:
220
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.14
DANN
Benign
0.48

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: rs2758886; hg19: chr6-39250837; API