rs7199513

Variant names:

• chr16-3723489-G-A
• rs7199513

Your query was ambiguous. Multiple possible variants found:

• chr16-3723489-G-A
• chr16-3723489-G-C

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 0.596 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.826 AC: 34233 AN: 41434

American (AMR) AF: 0.579 AC: 8822 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2218 AN: 3458

East Asian (EAS) AF: 0.862 AC: 4377 AN: 5080

South Asian (SAS) AF: 0.665 AC: 3187 AN: 4794

European-Finnish (FIN) AF: 0.520 AC: 5442 AN: 10470

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30250 AN: 67776

Other (OTH) AF: 0.585 AC: 1229 AN: 2102

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7199513; hg19: chr16-3773490;