rs16978810

Variant names:

• chr21-46068418-C-A
• rs16978810

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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 the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 184 gene

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: 0.0438 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

African (AFR) AF: 0.0354 AC: 1472 AN: 41530

American (AMR) AF: 0.0268 AC: 410 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.00870 AC: 42 AN: 4830

European-Finnish (FIN) AF: 0.112 AC: 1193 AN: 10620

Middle Eastern (MID) AF: 0.0240 AC: 7 AN: 292

European-Non Finnish (NFE) AF: 0.0497 AC: 3378 AN: 68026

Other (OTH) AF: 0.0331 AC: 70 AN: 2116

Alfa AF: 0.0453 Hom.: 107

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs16978810; hg19: chr21-47488332;