rs1945465

Positions:

• chr11-78645453-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 0.589 in 151,692 control chromosomes in the GnomAD database, including 28,385 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 0.59 (28385 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.78645453T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89368 AN: 151570 Hom.: 28394 Cov.: 33

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.589 AC: 89365 AN: 151692 Hom.: 28385 Cov.: 33 AF XY: 0.582 AC XY: 43151 AN XY: 74104

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.604

Alfa AF: 0.704 Hom.: 76278

Bravo AF: 0.574

Asia WGS AF: 0.345 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1945465; hg19: chr11-78356498;