rs6729693

Variant names:

• chr2-105972561-G-A
• rs6729693

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0870 AC: 3562 AN: 40966

American (AMR) AF: 0.110 AC: 1632 AN: 14864

Ashkenazi Jewish (ASJ) AF: 0.0488 AC: 169 AN: 3462

East Asian (EAS) AF: 0.236 AC: 1206 AN: 5116

South Asian (SAS) AF: 0.128 AC: 603 AN: 4712

European-Finnish (FIN) AF: 0.0609 AC: 641 AN: 10518

Middle Eastern (MID) AF: 0.0137 AC: 4 AN: 292

European-Non Finnish (NFE) AF: 0.0549 AC: 3709 AN: 67608

Other (OTH) AF: 0.0820 AC: 169 AN: 2060

Alfa AF: 0.0680 Hom.: 611

Bravo AF: 0.0854

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.77
DANN	Benign	0.50
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs6729693; hg19: chr2-106589017;