rs4399544

Variant names:

• chr16-20220513-G-A
• rs4399544

Your query was ambiguous. Multiple possible variants found:

• chr16-20220513-G-A
• chr16-20220513-G-C

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 0.475 in 151,958 control chromosomes in the GnomAD database, including 19,217 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 0.48 (19217 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 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: 0.476 AC: 72229 AN: 151840 Hom.: 19217 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.475 AC: 72240 AN: 151958 Hom.: 19217 Cov.: 32 AF XY: 0.476 AC XY: 35341 AN XY: 74246

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.530

Alfa AF: 0.515 Hom.: 3582

Bravo AF: 0.466

Asia WGS AF: 0.536 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	13
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4399544; hg19: chr16-20231835;