rs7100400

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 0.0349 in 152,176 control chromosomes in the GnomAD database, including 164 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 0.035 ( 164 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.387
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 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:
0.0349
AC:
5314
AN:
152058
Hom.:
163
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00884
Gnomad AMI
AF:
0.167
Gnomad AMR
AF:
0.0313
Gnomad ASJ
AF:
0.0179
Gnomad EAS
AF:
0.140
Gnomad SAS
AF:
0.0375
Gnomad FIN
AF:
0.0303
Gnomad MID
AF:
0.0190
Gnomad NFE
AF:
0.0435
Gnomad OTH
AF:
0.0306
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0349
AC:
5317
AN:
152176
Hom.:
164
Cov.:
31
AF XY:
0.0348
AC XY:
2588
AN XY:
74418
show subpopulations
Gnomad4 AFR
AF:
0.00881
Gnomad4 AMR
AF:
0.0313
Gnomad4 ASJ
AF:
0.0179
Gnomad4 EAS
AF:
0.141
Gnomad4 SAS
AF:
0.0374
Gnomad4 FIN
AF:
0.0303
Gnomad4 NFE
AF:
0.0435
Gnomad4 OTH
AF:
0.0331
Alfa
AF:
0.0391
Hom.:
81
Bravo
AF:
0.0343
Asia WGS
AF:
0.102
AC:
353
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.8
DANN
Benign
0.80

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: rs7100400; hg19: chr10-6124080; API