rs489095

Positions:

• chr5-4923516-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 0.484 in 152,184 control chromosomes in the GnomAD database, including 21,243 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 0.48 (21243 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 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: 0.484 AC: 73629 AN: 152066 Hom.: 21247 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.484 AC: 73641 AN: 152184 Hom.: 21243 Cov.: 33 AF XY: 0.479 AC XY: 35645 AN XY: 74400

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.0104

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.484

Alfa AF: 0.563 Hom.: 4385

Bravo AF: 0.460

Asia WGS AF: 0.213 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs489095; hg19: chr5-4923629;