rs12672644

Variant names:

• chr7-15090527-C-T
• rs12672644

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 0.124 in 152,080 control chromosomes in the GnomAD database, including 1,340 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 0.12 (1340 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 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: 0.124 AC: 18836 AN: 151962 Hom.: 1339 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.0902

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.0764

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.124 AC: 18851 AN: 152080 Hom.: 1340 Cov.: 32 AF XY: 0.128 AC XY: 9524 AN XY: 74336

African (AFR) AF: 0.138 AC: 5709 AN: 41506

American (AMR) AF: 0.203 AC: 3106 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0902 AC: 313 AN: 3470

East Asian (EAS) AF: 0.247 AC: 1276 AN: 5162

South Asian (SAS) AF: 0.0764 AC: 368 AN: 4814

European-Finnish (FIN) AF: 0.127 AC: 1345 AN: 10558

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0939 AC: 6382 AN: 67994

Other (OTH) AF: 0.128 AC: 270 AN: 2104

Alfa AF: 0.102 Hom.: 407

Bravo AF: 0.134

Asia WGS AF: 0.143 AC: 497 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.84
DANN	Benign	0.63
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs12672644; hg19: chr7-15130152;