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GeneBe

rs4950926

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 0.282 in 152,128 control chromosomes in the GnomAD database, including 7,596 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 0.28 ( 7575 hom., cov: 30)
Exomes 𝑓: 0.38 ( 21 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.405
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=-0.77).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.396 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:
0.282
AC:
42757
AN:
151762
Hom.:
7572
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0884
Gnomad AMI
AF:
0.642
Gnomad AMR
AF:
0.259
Gnomad ASJ
AF:
0.365
Gnomad EAS
AF:
0.0259
Gnomad SAS
AF:
0.214
Gnomad FIN
AF:
0.403
Gnomad MID
AF:
0.358
Gnomad NFE
AF:
0.400
Gnomad OTH
AF:
0.306
GnomAD4 exome
AF:
0.383
AC:
95
AN:
248
Hom.:
21
AF XY:
0.390
AC XY:
67
AN XY:
172
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.500
Gnomad4 ASJ exome
AF:
0.250
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.250
Gnomad4 FIN exome
AF:
0.419
Gnomad4 NFE exome
AF:
0.396
Gnomad4 OTH exome
AF:
0.333
GnomAD4 genome
AF:
0.282
AC:
42761
AN:
151880
Hom.:
7575
Cov.:
30
AF XY:
0.281
AC XY:
20855
AN XY:
74214
show subpopulations
Gnomad4 AFR
AF:
0.0884
Gnomad4 AMR
AF:
0.258
Gnomad4 ASJ
AF:
0.365
Gnomad4 EAS
AF:
0.0260
Gnomad4 SAS
AF:
0.214
Gnomad4 FIN
AF:
0.403
Gnomad4 NFE
AF:
0.400
Gnomad4 OTH
AF:
0.302
Alfa
AF:
0.297
Hom.:
1115
Bravo
AF:
0.264
Asia WGS
AF:
0.109
AC:
383
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
Cadd
Benign
11
Dann
Benign
0.83

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: rs4950926; hg19: chr1-203136666; COSMIC: COSV55144327; API