rs1494550

Variant names:

• chr16-24255283-T-C
• rs1494550

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.286 AC: 11842 AN: 41474

American (AMR) AF: 0.169 AC: 2592 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 743 AN: 3468

East Asian (EAS) AF: 0.148 AC: 767 AN: 5182

South Asian (SAS) AF: 0.247 AC: 1193 AN: 4822

European-Finnish (FIN) AF: 0.214 AC: 2266 AN: 10602

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18778 AN: 67994

Other (OTH) AF: 0.227 AC: 479 AN: 2112

Alfa AF: 0.259 Hom.: 6781

Bravo AF: 0.251

Asia WGS AF: 0.205 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.51
PhyloP100		0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1494550;

hg19: chr16-24266604;