chr7-12897630-C-G

Position:

• chr7-12897630-C-G

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 0.133 in 151,982 control chromosomes in the GnomAD database, including 2,071 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 0.13 (2071 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.12897630C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000229618	ENST00000638964.1	n.484+94898C>G		intron_variant		5
ENSG00000229618	ENST00000639998.1	n.483+139314C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20124 AN: 151864 Hom.: 2072 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.133 AC: 20138 AN: 151982 Hom.: 2071 Cov.: 32 AF XY: 0.131 AC XY: 9704 AN XY: 74302

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.0765

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.0673

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.0713

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0359 Hom.: 22

Bravo AF: 0.138

Asia WGS AF: 0.108 AC: 374 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17166499; hg19: chr7-12937255;