rs79076257

chr8-109232394-T-C

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 0.042 in 152,280 control chromosomes in the GnomAD database, including 182 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 0.042 (182 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

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 (NFE) allele frequency at 95% confidence interval = 0.0615 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: 0.0420 AC: 6390 AN: 152162 Hom.: 182 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.0230

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00476

Gnomad FIN AF: 0.0917

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0630

Gnomad OTH AF: 0.0320

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

GnomAD4 genome AF: 0.0420 AC: 6393 AN: 152280 Hom.: 182 Cov.: 32 AF XY: 0.0419 AC XY: 3120 AN XY: 74452

Gnomad4 AFR AF: 0.0109

Gnomad4 AMR AF: 0.0317

Gnomad4 ASJ AF: 0.0230

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00477

Gnomad4 FIN AF: 0.0917

Gnomad4 NFE AF: 0.0631

Gnomad4 OTH AF: 0.0317

Alfa AF: 0.0541 Hom.: 33

Bravo AF: 0.0361

Asia WGS AF: 0.00549 AC: 21 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	1.3
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs79076257; hg19: chr8-110244623;