16-21215430-G-A

Variant names:

• chr16-21215430-G-A
• rs10492787

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.285 in 152,090 control chromosomes in the GnomAD database, including 6,451 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 (6451 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.391 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: 0.285 AC: 43381 AN: 151972 Hom.: 6447 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.285 AC: 43409 AN: 152090 Hom.: 6451 Cov.: 33 AF XY: 0.291 AC XY: 21634 AN XY: 74314

African (AFR) AF: 0.212 AC: 8781 AN: 41482

American (AMR) AF: 0.340 AC: 5196 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3468

East Asian (EAS) AF: 0.406 AC: 2097 AN: 5166

South Asian (SAS) AF: 0.396 AC: 1911 AN: 4824

European-Finnish (FIN) AF: 0.324 AC: 3416 AN: 10558

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 20016 AN: 68006

Other (OTH) AF: 0.304 AC: 641 AN: 2110

Alfa AF: 0.291 Hom.: 25571

Bravo AF: 0.281

Asia WGS AF: 0.429 AC: 1489 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	0.57
DANN	Benign	0.48
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10492787; hg19: chr16-21226751;