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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.528 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

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.553

Alfa AF: 0.583 Hom.: 10791

Bravo AF: 0.514

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1827213; hg19: chr16-56671841;