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GeneBe

rs10993994

chr10-46046326-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000663171.1(MSMB):c.-89T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151992 control chromosomes in the gnomAD Genomes database, including 22866 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 0.54 ( 22866 hom., cov: 33)

Consequence

MSMB
ENST00000663171.1 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0490

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 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
MSMBENST00000663171.1 linkuse as main transcriptc.-89T>C 5_prime_UTR_variant 2/5

Frequencies

GnomAD3 genomes
AF:
0.538
AC:
81774
AN:
151992
Hom.:
22866
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.390
Gnomad AMI
AF:
0.549
Gnomad AMR
AF:
0.593
Gnomad ASJ
AF:
0.516
Gnomad EAS
AF:
0.540
Gnomad SAS
AF:
0.413
Gnomad FIN
AF:
0.646
Gnomad MID
AF:
0.380
Gnomad NFE
AF:
0.609
Gnomad OTH
AF:
0.535
GnomAD4 exome
AF:
0.587
AC:
593099
AN:
1009578
Hom.:
177600
AF XY:
0.580
AC XY:
302844
AN XY:
521818
show subpopulations
Gnomad4 AFR exome
AF:
0.373
Gnomad4 AMR exome
AF:
0.659
Gnomad4 ASJ exome
AF:
0.507
Gnomad4 EAS exome
AF:
0.546
Gnomad4 SAS exome
AF:
0.427
Gnomad4 FIN exome
AF:
0.650
Gnomad4 NFE exome
AF:
0.612
Gnomad4 OTH exome
AF:
0.554
Alfa
AF:
0.584
Hom.:
52172
Bravo
AF:
0.534
Asia WGS
AF:
0.435
AC:
1513
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
2.5
Dann
Benign
0.60

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: rs10993994; hg19: chr10-51549496;