17-30749329-C-T

Position:

• chr17-30749329-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000290928 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUZ12P1	NR_024187.2	n.317-10162C>T		intron_variant
SUZ12P1	NR_144393.1	n.273+5960C>T		intron_variant
SUZ12P1	NR_144394.1	n.273+5960C>T		intron_variant
SUZ12P1	NR_144395.1	n.385+5960C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290928	ENST00000497969.6	n.722+5960C>T		intron_variant		1
ENSG00000290928	ENST00000582557.5	n.1015+5960C>T		intron_variant		1
ENSG00000290928	ENST00000578070.5	n.582+5960C>T		intron_variant		5

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

Gnomad4 AFR AF: 0.0849

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.0852

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0319 Hom.: 21

Bravo AF: 0.115

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.46
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11657662; hg19: chr17-29076347;