rs4979459

Variant names:

• chr9-114719386-G-T
• rs4979459

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.427 AC: 17690 AN: 41448

American (AMR) AF: 0.437 AC: 6672 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1983 AN: 3470

East Asian (EAS) AF: 0.571 AC: 2940 AN: 5146

South Asian (SAS) AF: 0.719 AC: 3467 AN: 4820

European-Finnish (FIN) AF: 0.532 AC: 5624 AN: 10572

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37429 AN: 67960

Other (OTH) AF: 0.482 AC: 1017 AN: 2110

Alfa AF: 0.531 Hom.: 23643

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs4979459; hg19: chr9-117481666;