rs1420263

Variant names:

• chr16-52165498-A-C
• rs1420263

Your query was ambiguous. Multiple possible variants found:

• chr16-52165498-A-C
• chr16-52165498-A-G

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 0.265 in 152,070 control chromosomes in the GnomAD database, including 5,855 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 0.26 (5855 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 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: 0.265 AC: 40260 AN: 151952 Hom.: 5845 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.265 AC: 40286 AN: 152070 Hom.: 5855 Cov.: 32 AF XY: 0.264 AC XY: 19607 AN XY: 74358

African (AFR) AF: 0.165 AC: 6832 AN: 41518

American (AMR) AF: 0.257 AC: 3914 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1400 AN: 3470

East Asian (EAS) AF: 0.129 AC: 669 AN: 5172

South Asian (SAS) AF: 0.293 AC: 1410 AN: 4812

European-Finnish (FIN) AF: 0.261 AC: 2760 AN: 10574

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22105 AN: 67960

Other (OTH) AF: 0.306 AC: 644 AN: 2108

Alfa AF: 0.223 Hom.: 864

Bravo AF: 0.259

Asia WGS AF: 0.225 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	14
DANN	Benign	0.72
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1420263; hg19: chr16-52199410;