16-82191961-A-T

Position:

• chr16-82191961-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.483 in 152,016 control chromosomes in the GnomAD database, including 22,795 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 0.48 (22795 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

ACMG classification

Verdict is Benign. Variant got -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 = 0.85 is higher than 0.05.

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: 0.482 AC: 73276 AN: 151900 Hom.: 22730 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.483 AC: 73400 AN: 152016 Hom.: 22795 Cov.: 32 AF XY: 0.492 AC XY: 36535 AN XY: 74284

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.426

Alfa AF: 0.191 Hom.: 375

Bravo AF: 0.512

Asia WGS AF: 0.589 AC: 2048 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	2.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1862819; hg19: chr16-82225566;