rs10505710

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 0.0375 in 152,326 control chromosomes in the GnomAD database, including 279 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 0.038 ( 279 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0390
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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 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:
0.0375
AC:
5702
AN:
152208
Hom.:
276
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.102
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0290
Gnomad ASJ
AF:
0.00259
Gnomad EAS
AF:
0.114
Gnomad SAS
AF:
0.0447
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.00184
Gnomad OTH
AF:
0.0416
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0375
AC:
5713
AN:
152326
Hom.:
279
Cov.:
33
AF XY:
0.0377
AC XY:
2807
AN XY:
74496
show subpopulations
Gnomad4 AFR
AF:
0.102
Gnomad4 AMR
AF:
0.0292
Gnomad4 ASJ
AF:
0.00259
Gnomad4 EAS
AF:
0.113
Gnomad4 SAS
AF:
0.0453
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00184
Gnomad4 OTH
AF:
0.0412
Alfa
AF:
0.0144
Hom.:
19
Bravo
AF:
0.0427
Asia WGS
AF:
0.0660
AC:
229
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
13
DANN
Benign
0.85

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: rs10505710; hg19: chr8-140300665; API