rs2256700

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 0.132 in 152,120 control chromosomes in the GnomAD database, including 1,951 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 0.13 ( 1951 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.985
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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 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:
0.132
AC:
19995
AN:
152002
Hom.:
1951
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.266
Gnomad AMI
AF:
0.0297
Gnomad AMR
AF:
0.106
Gnomad ASJ
AF:
0.0767
Gnomad EAS
AF:
0.0214
Gnomad SAS
AF:
0.116
Gnomad FIN
AF:
0.0593
Gnomad MID
AF:
0.0823
Gnomad NFE
AF:
0.0810
Gnomad OTH
AF:
0.128
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.132
AC:
20027
AN:
152120
Hom.:
1951
Cov.:
32
AF XY:
0.129
AC XY:
9627
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.266
Gnomad4 AMR
AF:
0.105
Gnomad4 ASJ
AF:
0.0767
Gnomad4 EAS
AF:
0.0214
Gnomad4 SAS
AF:
0.116
Gnomad4 FIN
AF:
0.0593
Gnomad4 NFE
AF:
0.0810
Gnomad4 OTH
AF:
0.130
Alfa
AF:
0.0908
Hom.:
1460
Bravo
AF:
0.141
Asia WGS
AF:
0.102
AC:
355
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.1
DANN
Benign
0.62

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: rs2256700; hg19: chr10-101633447; API