rs1420239

Variant names:

• chr16-52842699-T-C
• rs1420239

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 0.19 in 152,154 control chromosomes in the GnomAD database, including 3,535 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 0.19 (3535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28965 AN: 152036 Hom.: 3538 Cov.: 32

Gnomad AFR AF: 0.0554

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.190 AC: 28946 AN: 152154 Hom.: 3535 Cov.: 32 AF XY: 0.186 AC XY: 13820 AN XY: 74366

African (AFR) AF: 0.0553 AC: 2296 AN: 41548

American (AMR) AF: 0.181 AC: 2772 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5176

South Asian (SAS) AF: 0.135 AC: 651 AN: 4816

European-Finnish (FIN) AF: 0.270 AC: 2855 AN: 10576

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18971 AN: 67974

Other (OTH) AF: 0.192 AC: 406 AN: 2112

Alfa AF: 0.254 Hom.: 5740

Bravo AF: 0.176

Asia WGS AF: 0.0730 AC: 253 AN: 3478

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	0.26
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1420239; hg19: chr16-52876611;