rs1362549

Positions:

• chr16-52548863-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.31 (2328 hom., cov: 18)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.313 AC: 25016 AN: 80034 Hom.: 2324 Cov.: 18

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.426

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.313 AC: 25025 AN: 80036 Hom.: 2328 Cov.: 18 AF XY: 0.307 AC XY: 11894 AN XY: 38704

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.341

Alfa AF: 0.175 Hom.: 205

Bravo AF: 0.165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.031
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1362549; hg19: chr16-52582775;