rs8069976

Positions:

• chr17-78353769-C-A
• chr17-78353769-C-G

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 0.17 in 152,156 control chromosomes in the GnomAD database, including 2,291 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 0.17 (2291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25890 AN: 152036 Hom.: 2291 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.170 AC: 25892 AN: 152156 Hom.: 2291 Cov.: 32 AF XY: 0.170 AC XY: 12635 AN XY: 74388

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.184

Alfa AF: 0.176 Hom.: 404

Bravo AF: 0.172

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8069976; hg19: chr17-76349850;