rs7296859

Variant names:

• chr12-6784998-C-G
• rs7296859

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 0.73 in 152,092 control chromosomes in the GnomAD database, including 41,282 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 0.73 (41282 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110900 AN: 151974 Hom.: 41231 Cov.: 32

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.730 AC: 111007 AN: 152092 Hom.: 41282 Cov.: 32 AF XY: 0.728 AC XY: 54099 AN XY: 74336

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.701

Alfa AF: 0.708 Hom.: 3549

Bravo AF: 0.732

Asia WGS AF: 0.680 AC: 2370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7296859; hg19: chr12-6894164;