rs7199513

chr16-3723489-G-Achr16-3723489-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 0.596 in 151,560 control chromosomes in the GnomAD database, including 29,103 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 0.60 (29103 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.84 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: 0.596 AC: 90227 AN: 151440 Hom.: 29051 Cov.: 29

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.596 AC: 90343 AN: 151560 Hom.: 29103 Cov.: 29 AF XY: 0.601 AC XY: 44534 AN XY: 74040

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.862

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.585

Alfa AF: 0.516 Hom.: 2582

Bravo AF: 0.610

Asia WGS AF: 0.739 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.64
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7199513; hg19: chr16-3773490;