17-70315539-C-T

Position:

• chr17-70315539-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 0.45 in 151,896 control chromosomes in the GnomAD database, including 15,466 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 0.45 (15466 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.70315539C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267109	ENST00000592809.1	n.177-2151G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68309 AN: 151780 Hom.: 15447 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.450 AC: 68358 AN: 151896 Hom.: 15466 Cov.: 31 AF XY: 0.447 AC XY: 33178 AN XY: 74204

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.436

Alfa AF: 0.448 Hom.: 1882

Bravo AF: 0.456

Asia WGS AF: 0.468 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs312736; hg19: chr17-68311680;