16-79957119-T-G

Variant names:

• chr16-79957119-T-G
• rs4461087

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 0.752 in 152,038 control chromosomes in the GnomAD database, including 43,270 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 0.75 (43270 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.81 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: 0.752 AC: 114198 AN: 151920 Hom.: 43239 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.752 AC: 114284 AN: 152038 Hom.: 43270 Cov.: 32 AF XY: 0.752 AC XY: 55908 AN XY: 74316

Gnomad4 AFR AF: 0.668 AC: 0.668219 AN: 0.668219

Gnomad4 AMR AF: 0.822 AC: 0.821634 AN: 0.821634

Gnomad4 ASJ AF: 0.843 AC: 0.843318 AN: 0.843318

Gnomad4 EAS AF: 0.613 AC: 0.612534 AN: 0.612534

Gnomad4 SAS AF: 0.826 AC: 0.826132 AN: 0.826132

Gnomad4 FIN AF: 0.778 AC: 0.77824 AN: 0.77824

Gnomad4 NFE AF: 0.782 AC: 0.782352 AN: 0.782352

Gnomad4 OTH AF: 0.778 AC: 0.777778 AN: 0.777778

Alfa AF: 0.779 Hom.: 12305

Bravo AF: 0.750

Asia WGS AF: 0.726 AC: 2523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.13
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4461087; hg19: chr16-79991016;