16-11745470-G-T

Position:

• chr16-11745470-G-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 0.562 in 151,748 control chromosomes in the GnomAD database, including 24,310 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 0.56 (24310 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.11745470G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85185 AN: 151630 Hom.: 24286 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.562 AC: 85254 AN: 151748 Hom.: 24310 Cov.: 32 AF XY: 0.562 AC XY: 41658 AN XY: 74156

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.564

Alfa AF: 0.589 Hom.: 5489

Bravo AF: 0.542

Asia WGS AF: 0.504 AC: 1754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.58
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4780401; hg19: chr16-11839326;