rs16824978

Variant names:

• chr2-210807337-C-T
• rs16824978

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 0.293 in 151,724 control chromosomes in the GnomAD database, including 7,523 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 0.29 (7523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 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: 0.293 AC: 44439 AN: 151606 Hom.: 7511 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.293 AC: 44475 AN: 151724 Hom.: 7523 Cov.: 31 AF XY: 0.301 AC XY: 22329 AN XY: 74122

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.305

Alfa AF: 0.260 Hom.: 3270

Bravo AF: 0.303

Asia WGS AF: 0.620 AC: 2151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16824978; hg19: chr2-211672061;