chr15-66784609-A-G

Variant names:

• chr15-66784609-A-G
• rs4147407

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 0.107 in 152,152 control chromosomes in the GnomAD database, including 911 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 0.11 (911 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16287 AN: 152034 Hom.: 909 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0667

Gnomad SAS AF: 0.0708

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.107 AC: 16302 AN: 152152 Hom.: 911 Cov.: 32 AF XY: 0.106 AC XY: 7876 AN XY: 74400

African (AFR) AF: 0.101 AC: 4175 AN: 41514

American (AMR) AF: 0.0749 AC: 1145 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3468

East Asian (EAS) AF: 0.0665 AC: 343 AN: 5160

South Asian (SAS) AF: 0.0721 AC: 348 AN: 4824

European-Finnish (FIN) AF: 0.115 AC: 1222 AN: 10602

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8406 AN: 67986

Other (OTH) AF: 0.0904 AC: 191 AN: 2112

Alfa AF: 0.115 Hom.: 1290

Bravo AF: 0.104

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.067
DANN	Benign	0.77
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4147407; hg19: chr15-67076947;