rs6662844

chr1-183525318-G-A

Variant summary

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

The NM_001375584.1(SMG7):c.313-1278G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,916 control chromosomes in the GnomAD database, including 20,109 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 0.51 (20109 hom., cov: 31)
• Consequence: SMG7 NM_001375584.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

Genes affected

SMG7 (HGNC:16792): (SMG7 nonsense mediated mRNA decay factor) This gene encodes a protein that is essential for nonsense-mediated mRNA decay (NMD); a process whereby transcripts with premature termination codons are targeted for rapid degradation by a mRNA decay complex. The mRNA decay complex consists, in part, of this protein along with proteins SMG5 and UPF1. The N-terminal domain of this protein is thought to mediate its association with SMG5 or UPF1 while the C-terminal domain interacts with the mRNA decay complex. This protein may therefore couple changes in UPF1 phosphorylation state to the degradation of NMD-candidate transcripts. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMG7	NM_001375584.1	c.313-1278G>A		intron_variant		ENST00000688051.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMG7	ENST00000688051.1	c.313-1278G>A		intron_variant			NM_001375584.1	P4

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77822 AN: 151798 Hom.: 20078 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.500

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.513 AC: 77897 AN: 151916 Hom.: 20109 Cov.: 31 AF XY: 0.515 AC XY: 38208 AN XY: 74236

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.500

Alfa AF: 0.483 Hom.: 24443

Bravo AF: 0.524

Asia WGS AF: 0.587 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.46
Dann	Benign	0.40

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: rs6662844; hg19: chr1-183494453;