16-51667187-G-A

Variant names:

• chr16-51667187-G-A
• rs10521243

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 0.076 in 151,982 control chromosomes in the GnomAD database, including 1,283 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 0.076 (1283 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 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: 0.0758 AC: 11517 AN: 151864 Hom.: 1281 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0268

Gnomad ASJ AF: 0.0205

Gnomad EAS AF: 0.0483

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.0000951

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00407

Gnomad OTH AF: 0.0566

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

GnomAD4 genome AF: 0.0760 AC: 11546 AN: 151982 Hom.: 1283 Cov.: 32 AF XY: 0.0740 AC XY: 5493 AN XY: 74254

African (AFR) AF: 0.246 AC: 10201 AN: 41444

American (AMR) AF: 0.0267 AC: 408 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0205 AC: 71 AN: 3468

East Asian (EAS) AF: 0.0486 AC: 251 AN: 5162

South Asian (SAS) AF: 0.0422 AC: 203 AN: 4810

European-Finnish (FIN) AF: 0.0000951 AC: 1 AN: 10520

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00407 AC: 277 AN: 68000

Other (OTH) AF: 0.0560 AC: 118 AN: 2108

Alfa AF: 0.0160 Hom.: 72

Bravo AF: 0.0840

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.4
DANN	Benign	0.75
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10521243; hg19: chr16-51701098;