rs12669076

Variant names:

• chr7-96785743-C-T
• rs12669076

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 0.245 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.148 AC: 6129 AN: 41496

American (AMR) AF: 0.239 AC: 3657 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1014 AN: 3472

East Asian (EAS) AF: 0.114 AC: 589 AN: 5180

South Asian (SAS) AF: 0.302 AC: 1456 AN: 4818

European-Finnish (FIN) AF: 0.358 AC: 3781 AN: 10550

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19900 AN: 67966

Other (OTH) AF: 0.253 AC: 536 AN: 2116

Alfa AF: 0.272 Hom.: 18393

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs12669076; hg19: chr7-96415055;