rs1420198

Variant names:

• chr16-52289283-A-G
• rs1420198

Your query was ambiguous. Multiple possible variants found:

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

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 0.248 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.373 AC: 15179 AN: 40690

American (AMR) AF: 0.240 AC: 3662 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1119 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1100 AN: 5164

South Asian (SAS) AF: 0.275 AC: 1325 AN: 4816

European-Finnish (FIN) AF: 0.164 AC: 1739 AN: 10588

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.185 AC: 12598 AN: 67980

Other (OTH) AF: 0.241 AC: 507 AN: 2104

Alfa AF: 0.209 Hom.: 4030

Bravo AF: 0.258

Asia WGS AF: 0.273 AC: 948 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1420198; hg19: chr16-52323195;