17-30755316-G-C

Variant names:

• chr17-30755316-G-C
• rs9898084
• ENST00000497969.6:n.723-2856G>C

Variant summary

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

The ENST00000497969.6(ENSG00000290928):​n.723-2856G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,142 control chromosomes in the GnomAD database, including 1,504 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 0.14 (1504 hom., cov: 32)
• Consequence: ENSG00000290928 ENST00000497969.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 12 publications found

Genes affected

ENSG00000290928 (HGNC:):

SUZ12P1 (HGNC:32421): (SUZ12 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUZ12P1	NR_024187.2	n.317-4175G>C		intron_variant	Intron 3 of 7
SUZ12P1	NR_144393.1	n.274-4175G>C		intron_variant	Intron 2 of 6
SUZ12P1	NR_144394.1	n.274-4175G>C		intron_variant	Intron 2 of 8
SUZ12P1	NR_144395.1	n.386-4175G>C		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290928	ENST00000497969.6	n.723-2856G>C		intron_variant	Intron 5 of 5	1
ENSG00000290928	ENST00000582557.5	n.1016-4175G>C		intron_variant	Intron 3 of 6	1
ENSG00000290928	ENST00000578070.5	n.583-11187G>C		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20608 AN: 152024 Hom.: 1499 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.136 AC: 20643 AN: 152142 Hom.: 1504 Cov.: 32 AF XY: 0.136 AC XY: 10104 AN XY: 74386

African (AFR) AF: 0.167 AC: 6946 AN: 41498

American (AMR) AF: 0.163 AC: 2491 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3470

East Asian (EAS) AF: 0.132 AC: 683 AN: 5168

South Asian (SAS) AF: 0.249 AC: 1202 AN: 4826

European-Finnish (FIN) AF: 0.0848 AC: 899 AN: 10602

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7600 AN: 68002

Other (OTH) AF: 0.133 AC: 280 AN: 2108

Alfa AF: 0.121 Hom.: 141

Bravo AF: 0.142

Asia WGS AF: 0.202 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.21
PhyloP100		0.012
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: rs9898084; hg19: chr17-29082334;