rs12669076

Positions:

• chr7-96785743-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 0.245 in 152,098 control chromosomes in the GnomAD database, including 4,980 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 0.25 (4980 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37290 AN: 151980 Hom.: 4976 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.245 AC: 37315 AN: 152098 Hom.: 4980 Cov.: 32 AF XY: 0.249 AC XY: 18513 AN XY: 74350

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.253

Alfa AF: 0.277 Hom.: 8275

Bravo AF: 0.229

Asia WGS AF: 0.197 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.69
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12669076; hg19: chr7-96415055;