rs6464268

chr7-152684065-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 0.23 in 151,278 control chromosomes in the GnomAD database, including 5,284 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 0.23 (5284 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 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: 0.229 AC: 34664 AN: 151158 Hom.: 5272 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0868

Gnomad MID AF: 0.144

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.230 AC: 34720 AN: 151278 Hom.: 5284 Cov.: 32 AF XY: 0.227 AC XY: 16755 AN XY: 73836

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0868

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.218

Alfa AF: 0.151 Hom.: 4233

Bravo AF: 0.254

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.21
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6464268; hg19: chr7-152381150;