16-30308986-G-T

Position:

• chr16-30308986-G-T

Variant summary

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

The NR_002453.5(SMG1P5):​n.401-3033C>A variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.325 in 152,024 control chromosomes in the GnomAD database, including 10,166 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 0.32 (10166 hom., cov: 31)
• Consequence: SMG1P5 NR_002453.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.29

Genes affected

SMG1P5 (HGNC:49862): (SMG1 pseudogene 5)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMG1P5	NR_002453.5	n.401-3033C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMG1P5	ENST00000411546.5	n.422-3033C>A		intron_variant, non_coding_transcript_variant		1
SMG1P5	ENST00000529428.5	n.81-3033C>A		intron_variant, non_coding_transcript_variant
SMG1P5	ENST00000691460.1	n.400-3033C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49370 AN: 151904 Hom.: 10165 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.0775

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.325 AC: 49363 AN: 152024 Hom.: 10166 Cov.: 31 AF XY: 0.319 AC XY: 23687 AN XY: 74276

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.0774

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.330

Alfa AF: 0.305 Hom.: 1563

Bravo AF: 0.304

Asia WGS AF: 0.165 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	20
DANN	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4471699; hg19: chr16-30320307;