rs1420198

Positions:

• chr16-52289283-A-G
• chr16-52289283-A-T

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 0.248 in 151,262 control chromosomes in the GnomAD database, including 5,238 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 0.25 (5238 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

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 (AFR) allele frequency at 95% confidence interval = 0.368 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: 0.247 AC: 37387 AN: 151142 Hom.: 5221 Cov.: 31

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.248 AC: 37443 AN: 151262 Hom.: 5238 Cov.: 31 AF XY: 0.246 AC XY: 18233 AN XY: 73980

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.241

Alfa AF: 0.208 Hom.: 2566

Bravo AF: 0.258

Asia WGS AF: 0.273 AC: 948 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1420198; hg19: chr16-52323195;