rs312707

Positions:

• chr17-70304495-C-A

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 0.267 in 151,998 control chromosomes in the GnomAD database, including 5,665 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 0.27 (5665 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536

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 = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40654 AN: 151882 Hom.: 5665 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.267 AC: 40653 AN: 151998 Hom.: 5665 Cov.: 31 AF XY: 0.274 AC XY: 20385 AN XY: 74284

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.241

Alfa AF: 0.258 Hom.: 942

Bravo AF: 0.258

Asia WGS AF: 0.251 AC: 875 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	0.81
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: rs312707; hg19: chr17-68300636;