chr15-78557199-C-T

Position:

• chr15-78557199-C-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 0.695 in 150,256 control chromosomes in the GnomAD database, including 36,829 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 0.70 (36829 hom., cov: 27)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.78557199C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.695 AC: 104380 AN: 150144 Hom.: 36775 Cov.: 27

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.695 AC: 104493 AN: 150256 Hom.: 36829 Cov.: 27 AF XY: 0.699 AC XY: 51192 AN XY: 73208

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.708

Alfa AF: 0.598 Hom.: 3807

Bravo AF: 0.707

Asia WGS AF: 0.772 AC: 2678 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4275821; hg19: chr15-78849541;