rs2005219

Variant names:

• chr16-30129937-A-C
• rs2005219

Your query was ambiguous. Multiple possible variants found:

• chr16-30129937-A-C
• chr16-30129937-A-G

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 0.417 in 151,046 control chromosomes in the GnomAD database, including 14,022 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 0.42 (14022 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.416 AC: 62838 AN: 150920 Hom.: 13992 Cov.: 29

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.417 AC: 62930 AN: 151046 Hom.: 14022 Cov.: 29 AF XY: 0.414 AC XY: 30504 AN XY: 73756

African (AFR) AF: 0.563 AC: 23191 AN: 41202

American (AMR) AF: 0.376 AC: 5711 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1348 AN: 3462

East Asian (EAS) AF: 0.591 AC: 2952 AN: 4998

South Asian (SAS) AF: 0.267 AC: 1266 AN: 4750

European-Finnish (FIN) AF: 0.386 AC: 4037 AN: 10460

Middle Eastern (MID) AF: 0.368 AC: 103 AN: 280

European-Non Finnish (NFE) AF: 0.342 AC: 23168 AN: 67704

Other (OTH) AF: 0.398 AC: 837 AN: 2102

Alfa AF: 0.362 Hom.: 11521

Bravo AF: 0.429

Asia WGS AF: 0.435 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.54
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2005219; hg19: chr16-30141258;