rs12672644

Variant names:

• chr7-15090527-C-T
• rs12672644

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 0.124 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.124 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

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.0902

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.0764

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0939

Gnomad4 OTH AF: 0.128

Alfa AF: 0.101 Hom.: 355

Bravo AF: 0.134

Asia WGS AF: 0.143 AC: 497 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12672644; hg19: chr7-15130152;