rs6729693

Positions:

• chr2-105972561-G-A

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 0.0783 in 150,506 control chromosomes in the GnomAD database, including 640 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 0.078 (640 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 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: 0.0783 AC: 11769 AN: 150384 Hom.: 635 Cov.: 33

Gnomad AFR AF: 0.0873

Gnomad AMI AF: 0.0980

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0488

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0783 AC: 11784 AN: 150506 Hom.: 640 Cov.: 33 AF XY: 0.0803 AC XY: 5896 AN XY: 73432

Gnomad4 AFR AF: 0.0870

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0488

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.0549

Gnomad4 OTH AF: 0.0820

Alfa AF: 0.0660 Hom.: 453

Bravo AF: 0.0854

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.77
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6729693; hg19: chr2-106589017;