17-70320318-C-T

Position:

• chr17-70320318-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.115 in 152,114 control chromosomes in the GnomAD database, including 1,300 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 0.12 (1300 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.70320318C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267109	ENST00000592809.1	n.177-6930G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17559 AN: 151994 Hom.: 1299 Cov.: 32

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.115 AC: 17565 AN: 152114 Hom.: 1300 Cov.: 32 AF XY: 0.116 AC XY: 8589 AN XY: 74328

Gnomad4 AFR AF: 0.0324

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0914

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.161

Alfa AF: 0.101 Hom.: 221

Bravo AF: 0.115

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
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: rs16975551; hg19: chr17-68316459;