rs4429303

Variant names:

• chr16-87870648-C-G
• rs4429303

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 0.189 in 152,220 control chromosomes in the GnomAD database, including 2,895 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 (2895 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.24 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: 0.189 AC: 28807 AN: 152102 Hom.: 2889 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.189 AC: 28831 AN: 152220 Hom.: 2895 Cov.: 33 AF XY: 0.188 AC XY: 13961 AN XY: 74414

African (AFR) AF: 0.159 AC: 6590 AN: 41536

American (AMR) AF: 0.155 AC: 2366 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 993 AN: 3472

East Asian (EAS) AF: 0.138 AC: 716 AN: 5180

South Asian (SAS) AF: 0.252 AC: 1218 AN: 4830

European-Finnish (FIN) AF: 0.154 AC: 1629 AN: 10598

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14673 AN: 67996

Other (OTH) AF: 0.206 AC: 435 AN: 2112

Alfa AF: 0.194 Hom.: 385

Bravo AF: 0.184

Asia WGS AF: 0.202 AC: 700 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	4.2
DANN	Benign	0.32
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs4429303; hg19: chr16-87904254;