16-3063897-T-C

Position:

• chr16-3063897-T-C

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 0.425 in 151,962 control chromosomes in the GnomAD database, including 14,134 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 0.43 (14134 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64580 AN: 151844 Hom.: 14136 Cov.: 31

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.425 AC: 64599 AN: 151962 Hom.: 14134 Cov.: 31 AF XY: 0.431 AC XY: 32048 AN XY: 74286

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.453

Alfa AF: 0.420 Hom.: 8334

Bravo AF: 0.425

Asia WGS AF: 0.620 AC: 2156 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	6.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4786370; hg19: chr16-3113898;