15-66578996-A-G

Variant names:

• chr15-66578996-A-G
• rs6494584

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 0.944 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.956 AC: 39737 AN: 41570

American (AMR) AF: 0.902 AC: 13799 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3172 AN: 3470

East Asian (EAS) AF: 0.638 AC: 3306 AN: 5180

South Asian (SAS) AF: 0.847 AC: 4084 AN: 4820

European-Finnish (FIN) AF: 0.988 AC: 10500 AN: 10628

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.970 AC: 66016 AN: 68034

Other (OTH) AF: 0.932 AC: 1972 AN: 2116

Alfa AF: 0.942 Hom.: 6798

Bravo AF: 0.936

Asia WGS AF: 0.776 AC: 2700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.66
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs6494584; hg19: chr15-66871334;