7-152684065-A-G

Variant names:

• chr7-152684065-A-G
• rs6464268

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 0.23 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
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.431 AC: 17792 AN: 41240

American (AMR) AF: 0.288 AC: 4364 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 675 AN: 3462

East Asian (EAS) AF: 0.187 AC: 959 AN: 5118

South Asian (SAS) AF: 0.130 AC: 623 AN: 4788

European-Finnish (FIN) AF: 0.0868 AC: 902 AN: 10392

Middle Eastern (MID) AF: 0.148 AC: 43 AN: 290

European-Non Finnish (NFE) AF: 0.130 AC: 8791 AN: 67818

Other (OTH) AF: 0.218 AC: 457 AN: 2100

Alfa AF: 0.170 Hom.: 9663

Bravo AF: 0.254

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.76
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs6464268; hg19: chr7-152381150;