rs4147407

Positions:

• chr15-66784609-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 0.107 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0749

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.0665

Gnomad4 SAS AF: 0.0721

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.0904

Alfa AF: 0.117 Hom.: 1019

Bravo AF: 0.104

Asia WGS AF: 0.0640 AC: 221 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	0.067
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4147407; hg19: chr15-67076947;