rs79323383

Positions:

• chr8-120839185-T-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 0.0499 in 152,230 control chromosomes in the GnomAD database, including 422 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 0.050 (422 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 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: 0.0498 AC: 7574 AN: 152112 Hom.: 415 Cov.: 32

Gnomad AFR AF: 0.0267

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0312

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0260

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0499 AC: 7595 AN: 152230 Hom.: 422 Cov.: 32 AF XY: 0.0545 AC XY: 4060 AN XY: 74454

Gnomad4 AFR AF: 0.0267

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0312

Gnomad4 NFE AF: 0.0260

Gnomad4 OTH AF: 0.0710

Alfa AF: 0.0379 Hom.: 34

Bravo AF: 0.0598

Asia WGS AF: 0.149 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.60
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs79323383; hg19: chr8-121851425;