rs216416

Variant names:

• chr17-30608627-G-A
• rs216416

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546
• Publications: 6 publications found

Genes affected

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

ENSG00000214719 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SMURF2P1		n.30608627G>A		intragenic_variant
SMURF2P1-LRRC37BP1	NR_015341.2	n.519+65G>A		intron_variant	Intron 4 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000214719	ENST00000398849.7	n.520+65G>A		intron_variant	Intron 4 of 8	2
ENSG00000214719	ENST00000431308.5	n.153+65G>A		intron_variant	Intron 2 of 5	5
ENSG00000214719	ENST00000440026.2	n.500+65G>A		intron_variant	Intron 3 of 5	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

African (AFR) AF: 0.301 AC: 6311 AN: 20942

American (AMR) AF: 0.174 AC: 3177 AN: 18272

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 1963 AN: 15110

East Asian (EAS) AF: 0.156 AC: 5010 AN: 32210

South Asian (SAS) AF: 0.180 AC: 6670 AN: 37128

European-Finnish (FIN) AF: 0.0872 AC: 2481 AN: 28464

Middle Eastern (MID) AF: 0.127 AC: 340 AN: 2676

European-Non Finnish (NFE) AF: 0.122 AC: 77824 AN: 637774

Other (OTH) AF: 0.143 AC: 5348 AN: 37412

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

African (AFR) AF: 0.295 AC: 11979 AN: 40560

American (AMR) AF: 0.184 AC: 2758 AN: 14968

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 434 AN: 3440

East Asian (EAS) AF: 0.127 AC: 650 AN: 5102

South Asian (SAS) AF: 0.197 AC: 924 AN: 4702

European-Finnish (FIN) AF: 0.0867 AC: 893 AN: 10298

Middle Eastern (MID) AF: 0.138 AC: 40 AN: 290

European-Non Finnish (NFE) AF: 0.116 AC: 7768 AN: 67240

Other (OTH) AF: 0.161 AC: 332 AN: 2056

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
PhyloP100		-0.55
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs216416; hg19: chr17-28935645;