ENST00000497969.6:n.722+5960C>T

Variant names:

• chr17-30749329-C-T
• rs11657662
• ENST00000497969.6:n.722+5960C>T

Variant summary

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

The ENST00000497969.6(ENSG00000290928):​n.722+5960C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,002 control chromosomes in the GnomAD database, including 1,045 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 0.11 (1045 hom., cov: 31)
• Consequence: ENSG00000290928 ENST00000497969.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 9 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=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000497969.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUZ12P1	NR_024187.2		n.317-10162C>T		intron	N/A
	SUZ12P1	NR_144393.1		n.273+5960C>T		intron	N/A
	SUZ12P1	NR_144394.1		n.273+5960C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290928	ENST00000497969.6	TSL:1	n.722+5960C>T		intron	N/A
	ENSG00000290928	ENST00000582557.5	TSL:1	n.1015+5960C>T		intron	N/A
	ENSG00000290928	ENST00000578070.5	TSL:5	n.582+5960C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17018 AN: 151882 Hom.: 1042 Cov.: 31

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.0852

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.112 AC: 17044 AN: 152002 Hom.: 1045 Cov.: 31 AF XY: 0.114 AC XY: 8452 AN XY: 74300

African (AFR) AF: 0.0849 AC: 3521 AN: 41452

American (AMR) AF: 0.156 AC: 2374 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3462

East Asian (EAS) AF: 0.133 AC: 686 AN: 5172

South Asian (SAS) AF: 0.250 AC: 1201 AN: 4806

European-Finnish (FIN) AF: 0.0852 AC: 900 AN: 10558

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7584 AN: 67976

Other (OTH) AF: 0.112 AC: 236 AN: 2110

Alfa AF: 0.0355 Hom.: 23

Bravo AF: 0.115

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.46
DANN	Benign	0.42
PhyloP100		-1.4
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: rs11657662; hg19: chr17-29076347;