rs7397470

Variant names:

• chr12-64403625-T-C
• rs7397470

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 0.193 in 152,260 control chromosomes in the GnomAD database, including 3,587 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 0.19 (3587 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 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: 0.193 AC: 29419 AN: 152142 Hom.: 3589 Cov.: 33

Gnomad AFR AF: 0.0486

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.193 AC: 29412 AN: 152260 Hom.: 3587 Cov.: 33 AF XY: 0.196 AC XY: 14556 AN XY: 74454

Gnomad4 AFR AF: 0.0484

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.189

Alfa AF: 0.244 Hom.: 7904

Bravo AF: 0.183

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7397470; hg19: chr12-64797405;