rs1549922

Positions:

• chr5-159304540-G-A

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 0.56 in 151,986 control chromosomes in the GnomAD database, including 24,276 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 0.56 (24276 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 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: 0.560 AC: 85029 AN: 151866 Hom.: 24228 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.560 AC: 85130 AN: 151986 Hom.: 24276 Cov.: 31 AF XY: 0.562 AC XY: 41734 AN XY: 74270

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.607

Alfa AF: 0.536 Hom.: 6784

Bravo AF: 0.580

Asia WGS AF: 0.658 AC: 2285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.77
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1549922; hg19: chr5-158731548;