rs16998312

Variant names:

• chr21-19083933-C-G
• rs16998312

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 0.0722 in 152,146 control chromosomes in the GnomAD database, including 622 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 0.072 (622 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 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: 0.0722 AC: 10983 AN: 152028 Hom.: 622 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0300

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.0218

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0465

Gnomad OTH AF: 0.0503

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

GnomAD4 genome AF: 0.0722 AC: 10987 AN: 152146 Hom.: 622 Cov.: 32 AF XY: 0.0683 AC XY: 5075 AN XY: 74354

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0300

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.0218

Gnomad4 SAS AF: 0.0324

Gnomad4 FIN AF: 0.0162

Gnomad4 NFE AF: 0.0465

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0609 Hom.: 44

Bravo AF: 0.0771

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16998312; hg19: chr21-20456251;