rs1879553

chr3-118896616-A-G

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 0.0749 in 152,072 control chromosomes in the GnomAD database, including 504 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 0.075 (504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 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: 0.0749 AC: 11381 AN: 151952 Hom.: 502 Cov.: 32

Gnomad AFR AF: 0.0469

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0807

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.0790

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

GnomAD4 genome AF: 0.0749 AC: 11392 AN: 152072 Hom.: 504 Cov.: 32 AF XY: 0.0738 AC XY: 5485 AN XY: 74348

Gnomad4 AFR AF: 0.0467

Gnomad4 AMR AF: 0.0778

Gnomad4 ASJ AF: 0.0882

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.0812

Gnomad4 FIN AF: 0.0442

Gnomad4 NFE AF: 0.0895

Gnomad4 OTH AF: 0.0801

Alfa AF: 0.0877 Hom.: 799

Bravo AF: 0.0778

Asia WGS AF: 0.0900 AC: 310 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.8
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1879553; hg19: chr3-118615463;