17-30608627-G-T

Variant names:

• chr17-30608627-G-T
• rs216416

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The variant allele was found at a frequency of 0.0000012 in 830,980 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0000012 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMURF2P1		n.30608627G>T		intragenic_variant
SMURF2P1-LRRC37BP1	NR_015341.2	n.519+65G>T		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>T		intron_variant	Intron 4 of 8	2
ENSG00000214719	ENST00000431308.5	n.153+65G>T		intron_variant	Intron 2 of 5	5
ENSG00000214719	ENST00000440026.2	n.500+65G>T		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.00000120 AC: 1 AN: 830980 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 413508

African (AFR) AF: 0.00 AC: 0 AN: 21012

American (AMR) AF: 0.00 AC: 0 AN: 18300

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15126

East Asian (EAS) AF: 0.00 AC: 0 AN: 32230

South Asian (SAS) AF: 0.0000269 AC: 1 AN: 37216

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28480

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2680

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 638472

Other (OTH) AF: 0.00 AC: 0 AN: 37464

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-0.55

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;