rs12705393

Positions:

• chr7-106862953-A-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 0.191 in 152,218 control chromosomes in the GnomAD database, including 3,533 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 (3533 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29125 AN: 152100 Hom.: 3533 Cov.: 33

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.191 AC: 29131 AN: 152218 Hom.: 3533 Cov.: 33 AF XY: 0.192 AC XY: 14263 AN XY: 74428

Gnomad4 AFR AF: 0.0505

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.00983

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.194

Alfa AF: 0.168 Hom.: 681

Bravo AF: 0.182

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12705393; hg19: chr7-106503398;