rs12672644

Positions:

• chr7-15090527-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;