rs16978810

chr21-46068418-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0438 in 152,282 control chromosomes in the GnomAD database, including 184 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 0.044 (184 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0438 (6675/152282) while in subpopulation NFE AF= 0.0497 (3378/68026). AF 95% confidence interval is 0.0483. There are 184 homozygotes in gnomad4. There are 3346 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 183 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0438 AC: 6665 AN: 152164 Hom.: 183 Cov.: 33

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0269

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00890

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0496

Gnomad OTH AF: 0.0334

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

GnomAD4 genome AF: 0.0438 AC: 6675 AN: 152282 Hom.: 184 Cov.: 33 AF XY: 0.0449 AC XY: 3346 AN XY: 74472

Gnomad4 AFR AF: 0.0354

Gnomad4 AMR AF: 0.0268

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00870

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0497

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0451 Hom.: 96

Bravo AF: 0.0369

Asia WGS AF: 0.0100 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.6
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16978810; hg19: chr21-47488332;