rs1827213

Variant names:

• chr16-56637929-G-A
• rs1827213

Your query was ambiguous. Multiple possible variants found:

• chr16-56637929-G-A
• chr16-56637929-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 0.527 in 152,050 control chromosomes in the GnomAD database, including 23,096 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 0.53 (23096 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80191 AN: 151932 Hom.: 23091 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.527 AC: 80203 AN: 152050 Hom.: 23096 Cov.: 32 AF XY: 0.531 AC XY: 39496 AN XY: 74316

African (AFR) AF: 0.282 AC: 11717 AN: 41484

American (AMR) AF: 0.606 AC: 9253 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2113 AN: 3468

East Asian (EAS) AF: 0.484 AC: 2497 AN: 5154

South Asian (SAS) AF: 0.506 AC: 2436 AN: 4812

European-Finnish (FIN) AF: 0.687 AC: 7270 AN: 10580

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43063 AN: 67960

Other (OTH) AF: 0.553 AC: 1166 AN: 2110

Alfa AF: 0.580 Hom.: 12842

Bravo AF: 0.514

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.48
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1827213; hg19: chr16-56671841;