rs4879753

Positions:

• chr9-34143309-A-G
• chr9-34143309-A-T

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 0.307 in 149,430 control chromosomes in the GnomAD database, including 7,457 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 0.31 (7457 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 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: 0.307 AC: 45860 AN: 149342 Hom.: 7452 Cov.: 29

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.307 AC: 45899 AN: 149430 Hom.: 7457 Cov.: 29 AF XY: 0.307 AC XY: 22359 AN XY: 72812

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.307

Alfa AF: 0.332 Hom.: 1396

Bravo AF: 0.294

Asia WGS AF: 0.275 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4879753; hg19: chr9-34143307;