15-79683407-C-T

Variant names:

• chr15-79683407-C-T
• rs4778721

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 0.248 in 152,022 control chromosomes in the GnomAD database, including 4,981 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 0.25 (4981 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 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: 0.248 AC: 37639 AN: 151904 Hom.: 4974 Cov.: 33

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.248 AC: 37677 AN: 152022 Hom.: 4981 Cov.: 33 AF XY: 0.243 AC XY: 18090 AN XY: 74306

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.248

Alfa AF: 0.226 Hom.: 765

Bravo AF: 0.255

Asia WGS AF: 0.364 AC: 1265 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4778721; hg19: chr15-79975749;