rs10479469

chr5-180385668-A-Gchr5-180385668-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 0.371 in 151,476 control chromosomes in the GnomAD database, including 10,469 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 0.37 (10469 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

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 (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56101 AN: 151360 Hom.: 10458 Cov.: 28

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.371 AC: 56156 AN: 151476 Hom.: 10469 Cov.: 28 AF XY: 0.373 AC XY: 27609 AN XY: 73976

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.379

Alfa AF: 0.343 Hom.: 4984

Bravo AF: 0.383

Asia WGS AF: 0.393 AC: 1371 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	4.3
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10479469; hg19: chr5-179812668; COSMIC: COSV56994082;