rs216416

Positions:

• chr17-30608627-G-A
• chr17-30608627-G-T

Variant summary

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

The NR_015341.2(SMURF2P1-LRRC37BP1):​n.519+65G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 979,550 control chromosomes in the GnomAD database, including 10,658 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 0.17 (2685 hom., cov: 30)
  • Exomes 𝑓: 0.13 (7973 hom.)
• Consequence: SMURF2P1-LRRC37BP1 NR_015341.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

Genes affected

SMURF2P1 (HGNC:44402): (SMAD specific E3 ubiquitin protein ligase 2 pseudogene 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMURF2P1-LRRC37BP1	NR_015341.2	n.519+65G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMURF2P1	ENST00000514992.2	n.342+65G>A		intron_variant, non_coding_transcript_variant
	ENST00000579301.5	n.431+65G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.173 AC: 25839 AN: 149446 Hom.: 2670 Cov.: 30

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.141

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.163

GnomAD4 exome AF: 0.131 AC: 109124 AN: 829988 Hom.: 7973 AF XY: 0.131 AC XY: 54264 AN XY: 413040

Gnomad4 AFR exome AF: 0.301

Gnomad4 AMR exome AF: 0.174

Gnomad4 ASJ exome AF: 0.130

Gnomad4 EAS exome AF: 0.156

Gnomad4 SAS exome AF: 0.180

Gnomad4 FIN exome AF: 0.0872

Gnomad4 NFE exome AF: 0.122

Gnomad4 OTH exome AF: 0.143

GnomAD4 genome AF: 0.173 AC: 25895 AN: 149562 Hom.: 2685 Cov.: 30 AF XY: 0.171 AC XY: 12478 AN XY: 72936

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.0867

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.161

Alfa AF: 0.142 Hom.: 200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.5
DANN	Benign	0.58
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs216416; hg19: chr17-28935645;