rs3747238

chr22-45344215-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882

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]

ACMG classification

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
SMC1B	NM_148674.5	c.*341G>A		3_prime_UTR_variant	25/25	ENST00000357450.9
SMC1B	NM_001291501.2	c.*341G>A		3_prime_UTR_variant	23/23
SMC1B	XM_011530144.3	c.*341G>A		3_prime_UTR_variant	25/25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMC1B	ENST00000357450.9	c.*341G>A		3_prime_UTR_variant	25/25	5	NM_148674.5	P1

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60235 AN: 152054 Hom.: 14635 Cov.: 34

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

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

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

Other links and lift over

dbSNP: rs3747238; hg19: chr22-45740096;