rs7304896

Variant names:

• chr12-25265778-T-G
• rs7304896

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 0.112 in 152,160 control chromosomes in the GnomAD database, including 1,062 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 0.11 (1062 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.183 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: 0.112 AC: 17026 AN: 152042 Hom.: 1060 Cov.: 31

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0815

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.112 AC: 17035 AN: 152160 Hom.: 1062 Cov.: 31 AF XY: 0.115 AC XY: 8580 AN XY: 74392

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.0814

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.0899

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0985 Hom.: 161

Bravo AF: 0.107

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7304896; hg19: chr12-25418712;