rs7397470

Positions:

• chr12-64403625-T-C

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.64403625T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;