rs3747238

Variant summary

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

The NM_148674.5(SMC1B):​c.*341G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 162,354 control chromosomes in the GnomAD database, including 15,883 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 0.40 ( 14635 hom., cov: 34)
Exomes 𝑓: 0.49 ( 1248 hom. )

Consequence

SMC1B
NM_148674.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.882
Variant links:
Genes affected
SMC1B (HGNC:11112): (structural maintenance of chromosomes 1B) SMC1L2 belongs to a family of proteins required for chromatid cohesion and DNA recombination during meiosis and mitosis (3:Revenkova et al., 2001 [PubMed 11564881]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SMC1BNM_148674.5 linkuse as main transcriptc.*341G>A 3_prime_UTR_variant 25/25 ENST00000357450.9
SMC1BNM_001291501.2 linkuse as main transcriptc.*341G>A 3_prime_UTR_variant 23/23
SMC1BXM_011530144.3 linkuse as main transcriptc.*341G>A 3_prime_UTR_variant 25/25

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SMC1BENST00000357450.9 linkuse as main transcriptc.*341G>A 3_prime_UTR_variant 25/255 NM_148674.5 P1

Frequencies

GnomAD3 genomes
AF:
0.396
AC:
60235
AN:
152054
Hom.:
14635
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.111
Gnomad AMI
AF:
0.511
Gnomad AMR
AF:
0.442
Gnomad ASJ
AF:
0.495
Gnomad EAS
AF:
0.338
Gnomad SAS
AF:
0.327
Gnomad FIN
AF:
0.467
Gnomad MID
AF:
0.408
Gnomad NFE
AF:
0.551
Gnomad OTH
AF:
0.414
GnomAD4 exome
AF:
0.488
AC:
4971
AN:
10182
Hom.:
1248
Cov.:
0
AF XY:
0.496
AC XY:
2604
AN XY:
5248
show subpopulations
Gnomad4 AFR exome
AF:
0.118
Gnomad4 AMR exome
AF:
0.448
Gnomad4 ASJ exome
AF:
0.479
Gnomad4 EAS exome
AF:
0.436
Gnomad4 SAS exome
AF:
0.261
Gnomad4 FIN exome
AF:
0.464
Gnomad4 NFE exome
AF:
0.528
Gnomad4 OTH exome
AF:
0.440
GnomAD4 genome
AF:
0.396
AC:
60242
AN:
152172
Hom.:
14635
Cov.:
34
AF XY:
0.390
AC XY:
29030
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.111
Gnomad4 AMR
AF:
0.443
Gnomad4 ASJ
AF:
0.495
Gnomad4 EAS
AF:
0.337
Gnomad4 SAS
AF:
0.328
Gnomad4 FIN
AF:
0.467
Gnomad4 NFE
AF:
0.551
Gnomad4 OTH
AF:
0.408
Alfa
AF:
0.496
Hom.:
12214
Bravo
AF:
0.385
Asia WGS
AF:
0.264
AC:
916
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.75
DANN
Benign
0.29

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs3747238; hg19: chr22-45740096; API