chr4-12668766-G-A

Variant names:

• chr4-12668766-G-A
• rs7668124

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 0.463 in 151,666 control chromosomes in the GnomAD database, including 16,667 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 0.46 (16667 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 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: 0.463 AC: 70091 AN: 151546 Hom.: 16639 Cov.: 31

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.463 AC: 70159 AN: 151666 Hom.: 16667 Cov.: 31 AF XY: 0.470 AC XY: 34860 AN XY: 74126

African (AFR) AF: 0.500 AC: 20637 AN: 41302

American (AMR) AF: 0.486 AC: 7375 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1010 AN: 3472

East Asian (EAS) AF: 0.687 AC: 3540 AN: 5154

South Asian (SAS) AF: 0.675 AC: 3254 AN: 4820

European-Finnish (FIN) AF: 0.426 AC: 4485 AN: 10526

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28486 AN: 67890

Other (OTH) AF: 0.431 AC: 911 AN: 2112

Alfa AF: 0.434 Hom.: 6126

Bravo AF: 0.464

Asia WGS AF: 0.647 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.71
DANN	Benign	0.41
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs7668124; hg19: chr4-12670390;