15-78557199-C-T

Variant names:

• chr15-78557199-C-T
• rs4275821

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;