rs78979090

Variant names:

• chr5-120343753-C-G
• rs78979090

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 0.0375 in 152,110 control chromosomes in the GnomAD database, including 217 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 0.038 (217 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0374 AC: 5688 AN: 151992 Hom.: 213 Cov.: 32

Gnomad AFR AF: 0.0914

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0279

Gnomad ASJ AF: 0.0344

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00373

Gnomad FIN AF: 0.00482

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0479

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

GnomAD4 genome AF: 0.0375 AC: 5711 AN: 152110 Hom.: 217 Cov.: 32 AF XY: 0.0362 AC XY: 2689 AN XY: 74370

Gnomad4 AFR AF: 0.0917

Gnomad4 AMR AF: 0.0279

Gnomad4 ASJ AF: 0.0344

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00394

Gnomad4 FIN AF: 0.00482

Gnomad4 NFE AF: 0.0164

Gnomad4 OTH AF: 0.0474

Alfa AF: 0.0279 Hom.: 13

Bravo AF: 0.0418

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs78979090; hg19: chr5-119679448;