rs4979459

Variant names:

• chr9-114719386-G-T
• rs4979459

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 0.51 in 152,008 control chromosomes in the GnomAD database, including 20,117 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 0.51 (20117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.699 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: 0.510 AC: 77434 AN: 151892 Hom.: 20111 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.510 AC: 77486 AN: 152008 Hom.: 20117 Cov.: 32 AF XY: 0.511 AC XY: 37972 AN XY: 74300

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.482

Alfa AF: 0.524 Hom.: 1947

Bravo AF: 0.493

Asia WGS AF: 0.607 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4979459; hg19: chr9-117481666;