15-66578996-A-G

Position:

• chr15-66578996-A-G

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 0.944 in 152,314 control chromosomes in the GnomAD database, including 68,167 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 0.94 (68167 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143636 AN: 152196 Hom.: 68103 Cov.: 33

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.931

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

GnomAD4 genome AF: 0.944 AC: 143761 AN: 152314 Hom.: 68167 Cov.: 33 AF XY: 0.940 AC XY: 69998 AN XY: 74474

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.902

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.988

Gnomad4 NFE AF: 0.970

Gnomad4 OTH AF: 0.932

Alfa AF: 0.942 Hom.: 6444

Bravo AF: 0.936

Asia WGS AF: 0.776 AC: 2700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6494584; hg19: chr15-66871334;