7-86334718-T-C

Variant names:

• chr7-86334718-T-C
• rs12673599

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 0.893 in 151,582 control chromosomes in the GnomAD database, including 60,745 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 0.89 (60745 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135310 AN: 151464 Hom.: 60682 Cov.: 31

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.806

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.893 AC: 135430 AN: 151582 Hom.: 60745 Cov.: 31 AF XY: 0.894 AC XY: 66274 AN XY: 74102

African (AFR) AF: 0.966 AC: 40061 AN: 41468

American (AMR) AF: 0.882 AC: 13403 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2924 AN: 3454

East Asian (EAS) AF: 0.932 AC: 4803 AN: 5154

South Asian (SAS) AF: 0.879 AC: 4237 AN: 4820

European-Finnish (FIN) AF: 0.890 AC: 9423 AN: 10584

Middle Eastern (MID) AF: 0.808 AC: 236 AN: 292

European-Non Finnish (NFE) AF: 0.855 AC: 57815 AN: 67600

Other (OTH) AF: 0.868 AC: 1820 AN: 2096

Alfa AF: 0.862 Hom.: 28563

Bravo AF: 0.893

Asia WGS AF: 0.887 AC: 3085 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.7
DANN	Benign	0.81
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs12673599; hg19: chr7-85964034;