15-79570561-C-T

Variant names:

• chr15-79570561-C-T
• rs4778708

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.317 in 152,086 control chromosomes in the GnomAD database, including 8,158 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 0.32 (8158 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 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: 0.317 AC: 48234 AN: 151968 Hom.: 8151 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.317 AC: 48272 AN: 152086 Hom.: 8158 Cov.: 32 AF XY: 0.319 AC XY: 23704 AN XY: 74348

African (AFR) AF: 0.412 AC: 17097 AN: 41470

American (AMR) AF: 0.266 AC: 4072 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1266 AN: 3470

East Asian (EAS) AF: 0.574 AC: 2967 AN: 5170

South Asian (SAS) AF: 0.296 AC: 1425 AN: 4812

European-Finnish (FIN) AF: 0.297 AC: 3139 AN: 10560

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17286 AN: 67990

Other (OTH) AF: 0.299 AC: 632 AN: 2114

Alfa AF: 0.278 Hom.: 8131

Bravo AF: 0.322

Asia WGS AF: 0.394 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.58
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4778708; hg19: chr15-79862903;