rs45492607

chr16-52548864-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0226 in 65,272 control chromosomes in the GnomAD database, including 12 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 0.023 (12 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0226 (1473/65272) while in subpopulation AFR AF= 0.0503 (564/11220). AF 95% confidence interval is 0.0468. There are 12 homozygotes in gnomad4. There are 705 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 12 gene

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: 0.0226 AC: 1474 AN: 65280 Hom.: 12 Cov.: 0

Gnomad AFR AF: 0.0503

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0157

Gnomad ASJ AF: 0.0266

Gnomad EAS AF: 0.0130

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.00408

Gnomad MID AF: 0.0846

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0202

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

GnomAD4 genome AF: 0.0226 AC: 1473 AN: 65272 Hom.: 12 Cov.: 0 AF XY: 0.0223 AC XY: 705 AN XY: 31554

Gnomad4 AFR AF: 0.0503

Gnomad4 AMR AF: 0.0157

Gnomad4 ASJ AF: 0.0266

Gnomad4 EAS AF: 0.0130

Gnomad4 SAS AF: 0.0348

Gnomad4 FIN AF: 0.00408

Gnomad4 NFE AF: 0.0164

Gnomad4 OTH AF: 0.0202

Alfa AF: 0.0115 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.031
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45492607; hg19: chr16-52582776;