rs16990692

Positions:

• chr4-35044044-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;