7-12207003-G-C

Position:

• chr7-12207003-G-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 0.141 in 152,140 control chromosomes in the GnomAD database, including 1,715 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 0.14 (1715 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.12207003G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21403 AN: 152022 Hom.: 1712 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.141 AC: 21428 AN: 152140 Hom.: 1715 Cov.: 32 AF XY: 0.142 AC XY: 10550 AN XY: 74370

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.0836

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.133

Alfa AF: 0.0234 Hom.: 15

Bravo AF: 0.143

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13244354; hg19: chr7-12246629;