16-79655030-C-T

Variant names:

• chr16-79655030-C-T
• rs8048408

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 0.419 in 152,012 control chromosomes in the GnomAD database, including 14,397 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 0.42 (14397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.504 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: 0.420 AC: 63727 AN: 151894 Hom.: 14397 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.419 AC: 63740 AN: 152012 Hom.: 14397 Cov.: 32 AF XY: 0.420 AC XY: 31193 AN XY: 74302

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.426

Alfa AF: 0.419 Hom.: 2537

Bravo AF: 0.396

Asia WGS AF: 0.374 AC: 1299 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8048408; hg19: chr16-79688927;