rs16990692

Variant names:

• chr4-35044044-A-G
• rs16990692

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 0.32 in 152,112 control chromosomes in the GnomAD database, including 8,055 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 0.32 (8055 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -8.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 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: 0.319 AC: 48540 AN: 151994 Hom.: 8039 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.320 AC: 48603 AN: 152112 Hom.: 8055 Cov.: 32 AF XY: 0.313 AC XY: 23262 AN XY: 74378

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.341

Alfa AF: 0.311 Hom.: 1306

Bravo AF: 0.330

Asia WGS AF: 0.277 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.087
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16990692; hg19: chr4-35045666;