rs1494550

Variant names:

• chr16-24255283-T-C
• rs1494550

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 0.255 in 152,154 control chromosomes in the GnomAD database, including 5,187 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 0.26 (5187 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38806 AN: 152036 Hom.: 5171 Cov.: 33

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.255 AC: 38860 AN: 152154 Hom.: 5187 Cov.: 33 AF XY: 0.252 AC XY: 18756 AN XY: 74394

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.227

Alfa AF: 0.260 Hom.: 5198

Bravo AF: 0.251

Asia WGS AF: 0.205 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1494550; hg19: chr16-24266604;