rs12673393

Positions:

• chr7-96748728-G-A
• chr7-96748728-G-T

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 0.0823 in 152,238 control chromosomes in the GnomAD database, including 599 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 0.082 (599 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0823 AC: 12527 AN: 152120 Hom.: 597 Cov.: 33

Gnomad AFR AF: 0.0397

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0741

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0799

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0823 AC: 12528 AN: 152238 Hom.: 599 Cov.: 33 AF XY: 0.0827 AC XY: 6158 AN XY: 74442

Gnomad4 AFR AF: 0.0400

Gnomad4 AMR AF: 0.0739

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0799

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0977 Hom.: 434

Bravo AF: 0.0802

Asia WGS AF: 0.107 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12673393; hg19: chr7-96378040;