rs1362549

Variant names:

• chr16-52548863-A-T
• rs1362549

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;