rs6464268

Variant names:

• chr7-152684065-A-G
• rs6464268

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;