16-63921543-G-A

Variant names:

• chr16-63921543-G-A
• rs1381102

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 0.41 in 151,946 control chromosomes in the GnomAD database, including 12,962 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 0.41 (12962 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 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: 0.410 AC: 62239 AN: 151828 Hom.: 12953 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.410 AC: 62273 AN: 151946 Hom.: 12962 Cov.: 32 AF XY: 0.402 AC XY: 29870 AN XY: 74246

African (AFR) AF: 0.456 AC: 18882 AN: 41422

American (AMR) AF: 0.347 AC: 5306 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3470

East Asian (EAS) AF: 0.365 AC: 1880 AN: 5152

South Asian (SAS) AF: 0.381 AC: 1834 AN: 4814

European-Finnish (FIN) AF: 0.341 AC: 3597 AN: 10554

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28077 AN: 67948

Other (OTH) AF: 0.402 AC: 848 AN: 2108

Alfa AF: 0.408 Hom.: 18598

Bravo AF: 0.411

Asia WGS AF: 0.348 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.29
DANN	Benign	0.40
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1381102; hg19: chr16-63955447;